3EX7 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF EJC IN ITS TRANSITION STATE

Authors :   G. R. Andersen, K. H. Nielsen

Date :   16 Oct 08 (Deposition) - 09 Dec 08 (Release) - 13 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,F  (1x)
Biol. Unit 2: E,G,H,I,J  (1x)

Keywords :   Protein-Rna Complex, Mrna Processing, Mrna Splicing, Mrna Transport, Nonsense-Mediated Mrna Decay, Nucleus, Rna- Binding, Spliceosome, Transport, Alternative Splicing, Cytoplasm, Phosphoprotein, Acetylation, Atp-Binding, Helicase, Hydrolase, Nucleotide-Binding, Rrna Processing, Coiled Coil, Hydrolase/Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Nielsen, H. Chamieh, C. B. Andersen, F. Fredslund, K. Hamborg, H. Le Hir, G. R. Andersen
Mechanism Of Atp Turnover Inhibition In The Ejc
Rna V. 15 67 2009
PubMed-ID: 19033377 | Reference-DOI: 10.1261/RNA.1283109
(for further references see the PDB file header)

Molecule 1 - PROTEIN MAGO NASHI HOMOLOG
	Chains	:	A, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAGOH
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - RNA-BINDING PROTEIN 8A
	Chains	:	B, G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 51-174
	Gene	:	RBM8A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RNA-BINDING MOTIF PROTEIN 8A, RIBONUCLEOPROTEIN RBM8A, RNA-BINDING PROTEIN Y14, BINDER OF OVCA1-1, BOV-1

Molecule 3 - EUKARYOTIC INITIATION FACTOR 4A-III
	Chains	:	C, H
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	EIF4A3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3, ATP-DEPENDENT RNA HELICASE EIF4A-3, ATP- DEPENDENT RNA HELICASE DDX48, DEAD BOX PROTEIN 48, EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34, NUCLEAR MATRIX PROTEIN 265, HNMP 265

Molecule 4 - PROTEIN CASC3
	Chains	:	D, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 138-283
	Gene	:	CASC3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN, METASTATIC LYMPH NODE PROTEIN 51, PROTEIN MLN 51, PROTEIN BARENTSZ, BTZ

*Molecule 5 - RNA (5'-R(UPUPUPUPUPU)-3')*
	Chains	:	F, J
	Engineered	:	YES
	Other Details	:	POLY URACIL (SIGMA)
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	E	F	G	H	I	J
Biological Unit 1 (1x)	:	A	B	C	D		F
Biological Unit 2 (1x)	:					E		G	H	I	J

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AF3	2	Ligand/Ion	ALUMINUM FLUORIDE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	AF3	1	Ligand/Ion	ALUMINUM FLUORIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE C:40 , TYR C:56 , PHE C:58 , LYS C:60 , GLN C:65 , GLY C:85 , THR C:86 , GLY C:87 , LYS C:88 , THR C:89 , ALA C:90 , ASP C:342 , ARG C:370 , TYR C:371 , AF3 C:415 , MG C:416 , HOH C:421 , HOH C:497 , HOH C:508 , HOH C:569 , HOH C:572	BINDING SITE FOR RESIDUE ADP C 414
2	AC2	SOFTWARE	SER C:84 , GLY C:85 , LYS C:88 , GLU C:188 , ALA C:219 , GLY C:340 , ARG C:367 , ARG C:370 , ADP C:414 , MG C:416 , HOH C:417 , HOH C:461 , HOH C:569 , HOH C:570 , HOH C:571 , HOH C:572	BINDING SITE FOR RESIDUE AF3 C 415
3	AC3	SOFTWARE	THR C:89 , ADP C:414 , AF3 C:415 , HOH C:570 , HOH C:571 , HOH C:572	BINDING SITE FOR RESIDUE MG C 416
4	AC4	SOFTWARE	PHE H:40 , PHE H:58 , LYS H:60 , GLN H:65 , GLY H:85 , THR H:86 , GLY H:87 , LYS H:88 , THR H:89 , ALA H:90 , ASP H:342 , ARG H:370 , TYR H:371 , AF3 H:415 , MG H:416 , HOH H:456 , HOH H:489 , HOH H:492	BINDING SITE FOR RESIDUE ADP H 414
5	AC5	SOFTWARE	SER H:84 , GLY H:85 , LYS H:88 , GLU H:188 , ALA H:219 , GLY H:340 , ARG H:367 , ARG H:370 , ADP H:414 , MG H:416 , HOH H:419 , HOH H:421 , HOH H:489 , HOH H:490 , HOH H:491	BINDING SITE FOR RESIDUE AF3 H 415
6	AC6	SOFTWARE	THR H:89 , ASP H:187 , ADP H:414 , AF3 H:415 , HOH H:490 , HOH H:491 , HOH H:492	BINDING SITE FOR RESIDUE MG H 416

(no "SS Bond" information available for 3EX7)

(no "Cis Peptide Bond" information available for 3EX7)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071090	D	270	G	IF4A3_HUMAN	Disease (RCPS)	587777204	C/H	D	270	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071090	D	270	G	IF4A3_HUMAN	Disease (RCPS)	587777204	C	D	270	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071090	D	270	G	IF4A3_HUMAN	Disease (RCPS)	587777204	H	D	270	G

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A3_HUMAN	38-66	2	C:38-66 H:38-66
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM8A_HUMAN	73-151	2	B:73-151 G:73-151
3	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A3_HUMAN	185-193	2	C:185-193 H:185-193

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A3_HUMAN	38-66	1	C:38-66 -
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM8A_HUMAN	73-151	1	B:73-151 -
3	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A3_HUMAN	185-193	1	C:185-193 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	Q_MOTIF	PS51195	DEAD-box RNA helicase Q motif profile.	IF4A3_HUMAN	38-66	1	- H:38-66
2	RRM	PS50102	Eukaryotic RNA Recognition Motif (RRM) profile.	RBM8A_HUMAN	73-151	1	- G:73-151
3	DEAD_ATP_HELICASE	PS00039	DEAD-box subfamily ATP-dependent helicases signature.	IF4A3_HUMAN	185-193	1	- H:185-193

Asymmetric Unit (19, 38)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000264645	1a	ENSE00001517546	chr17:38296507-38297032	526	CASC3_HUMAN	1-77	77	0	-	-
1.2	ENST00000264645	2	ENSE00000720185	chr17:38297460-38297487	28	CASC3_HUMAN	78-87	10	0	-	-
1.3	ENST00000264645	3	ENSE00001120433	chr17:38297823-38297860	38	CASC3_HUMAN	87-99	13	0	-	-
1.4a	ENST00000264645	4a	ENSE00000863354	chr17:38318006-38318164	159	CASC3_HUMAN	100-152	53	0	-	-
1.5	ENST00000264645	5	ENSE00000863355	chr17:38318255-38318406	152	CASC3_HUMAN	153-203	51	2	D:172-194 I:167-194	23 28
1.6	ENST00000264645	6	ENSE00000863356	chr17:38318978-38319154	177	CASC3_HUMAN	203-262	60	2	D:216-249 I:216-249	34 34
1.7b	ENST00000264645	7b	ENSE00000863357	chr17:38319734-38320419	686	CASC3_HUMAN	262-491	230	0	-	-
1.8b	ENST00000264645	8b	ENSE00000863358	chr17:38323050-38323114	65	CASC3_HUMAN	491-512	22	0	-	-
1.9	ENST00000264645	9	ENSE00000900529	chr17:38323751-38323865	115	CASC3_HUMAN	513-551	39	0	-	-
1.10	ENST00000264645	10	ENSE00000950687	chr17:38324103-38324201	99	CASC3_HUMAN	551-584	34	0	-	-
1.11b	ENST00000264645	11b	ENSE00000900527	chr17:38324456-38324670	215	CASC3_HUMAN	584-655	72	0	-	-
1.12	ENST00000264645	12	ENSE00001322421	chr17:38325577-38325699	123	CASC3_HUMAN	656-696	41	0	-	-
1.13a	ENST00000264645	13a	ENSE00001350371	chr17:38325851-38325915	65	CASC3_HUMAN	697-703	7	0	-	-
1.13c	ENST00000264645	13c	ENSE00001350362	chr17:38326700-38328431	1732	CASC3_HUMAN	-	0	0	-	-

2.1	ENST00000269349	1	ENSE00001213025	chr17:78120938-78120592	347	IF4A3_HUMAN	1-57	57	2	C:22-57 H:22-57	36 36
2.2	ENST00000269349	2	ENSE00000949585	chr17:78118043-78117971	73	IF4A3_HUMAN	57-81	25	2	C:57-81 H:57-81	25 25
2.3	ENST00000269349	3	ENSE00000949586	chr17:78115647-78115581	67	IF4A3_HUMAN	81-103	23	2	C:81-103 H:81-103	23 23
2.4	ENST00000269349	4	ENSE00000949587	chr17:78115180-78115118	63	IF4A3_HUMAN	104-124	21	2	C:104-124 H:104-124	21 21
2.5	ENST00000269349	5	ENSE00001303885	chr17:78113939-78113807	133	IF4A3_HUMAN	125-169	45	2	C:125-169 H:125-169	45 45
2.6	ENST00000269349	6	ENSE00000949589	chr17:78113549-78113469	81	IF4A3_HUMAN	169-196	28	2	C:169-196 H:169-196	28 28
2.7	ENST00000269349	7	ENSE00000949591	chr17:78112961-78112820	142	IF4A3_HUMAN	196-243	48	2	C:196-243 H:196-243	48 48
2.8	ENST00000269349	8	ENSE00001212947	chr17:78112079-78111941	139	IF4A3_HUMAN	243-289	47	2	C:243-289 H:243-289	47 47
2.9	ENST00000269349	9	ENSE00001212937	chr17:78111300-78111185	116	IF4A3_HUMAN	290-328	39	2	C:290-328 H:290-328	39 39
2.10	ENST00000269349	10	ENSE00000949595	chr17:78110134-78110027	108	IF4A3_HUMAN	328-364	37	2	C:328-364 H:328-364	37 37
2.11	ENST00000269349	11	ENSE00001213013	chr17:78109930-78109803	128	IF4A3_HUMAN	364-407	44	2	C:364-407 H:364-407	44 44
2.12	ENST00000269349	12	ENSE00001318045	chr17:78109305-78109019	287	IF4A3_HUMAN	407-411	5	2	C:407-411 H:407-411	5 5

3.1a	ENST00000371470	1a	ENSE00001853117	chr1:53704282-53704033	250	MGN_HUMAN	1-30	30	2	A:3-30 E:5-30	28 26
3.2	ENST00000371470	2	ENSE00001735272	chr1:53701307-53701249	59	MGN_HUMAN	30-49	20	2	A:30-49 E:30-49	20 20
3.3b	ENST00000371470	3b	ENSE00001689792	chr1:53699324-53699214	111	MGN_HUMAN	50-86	37	2	A:50-86 E:50-86	37 37
3.4	ENST00000371470	4	ENSE00001064642	chr1:53694626-53694544	83	MGN_HUMAN	87-114	28	2	A:87-114 E:87-114	28 28
3.5c	ENST00000371470	5c	ENSE00001064645	chr1:53692816-53692564	253	MGN_HUMAN	114-146	33	2	A:114-146 E:114-146	33 33

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:144
 aligned with MGN_HUMAN | P61326 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:144
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142    
            MGN_HUMAN     3 SDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
               SCOP domains d3ex7a_ A: Mago nashi protein                                                                                                                    SCOP domains
               CATH domains 3ex7A00 A:3-146 Mago nashi protein                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeeeee....eeeeeee.hhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 3 (1) Exon 3.1a  PDB: A:3-30      -------------------Exon 3.3b  PDB: A:50-86              Exon 3.4  PDB: A:87-114     -------------------------------- Transcript 3 (1)
           Transcript 3 (2) ---------------------------Exon 3.2            ----------------------------------------------------------------Exon 3.5c  PDB: A:114-146         Transcript 3 (2)
                 3ex7 A   3 SDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142

Chain B from PDB  Type:PROTEIN  Length:94
 aligned with RBM8A_HUMAN | Q9Y5S9 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:94
                                    73        83        93       103       113       123       133       143       153    
          RBM8A_HUMAN    64 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 157
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ex7B00 B:64-157  [code=3.30.70.330, no name defined]                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee......hhhhhhhhhhh...eeeee.............eeeee.hhhhhhhhhhhhh.........eeee.ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------RRM  PDB: B:73-151 UniProt: 73-151                                             ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3ex7 B  64 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGPPKG 157
                                    73        83        93       103       113       123       133       143       153

Chain C from PDB  Type:PROTEIN  Length:392
 aligned with IF4A3_HUMAN | P38919 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                               411  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
          IF4A3_HUMAN    22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh..hhhhhhhhhhhh......hhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhh......eeeeee...hhhhhhhhhhh....eee..hhhhh....eeeeeee....hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee.hhhh.......eeeeee.....hhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhh..eee...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------Q_MOTIF  PDB: C:38-66        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1  PDB: C:22-57 UniProt: 1-57-----------------------Exon 2.3  PDB: C:81-103Exon 2.4             Exon 2.5  PDB: C:125-169 UniProt: 125-169    --------------------------Exon 2.7  PDB: C:196-243 UniProt: 196-243       ------------------------------------------------------------------------------------Exon 2.10  PDB: C:328-364            ------------------------------------------2.12 -- Transcript 2 (1)
           Transcript 2 (2) -----------------------------------Exon 2.2  PDB: C:57-81   ---------------------------------------------------------------------------------------Exon 2.6  PDB: C:169-196    ----------------------------------------------Exon 2.8  PDB: C:243-289 UniProt: 243-289      Exon 2.9  PDB: C:290-328               -----------------------------------Exon 2.11  PDB: C:364-407 UniProt: 364-407  ------ Transcript 2 (2)
                 3ex7 C  22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 413
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411

Chain D from PDB  Type:PROTEIN  Length:57
 aligned with CASC3_HUMAN | O15234 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:78
                                   181       191       201       211       221       231       241        
          CASC3_HUMAN   172 DDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHN 249
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................---------------------................hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.5  PDB: D:172-194        ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.6  PDB: D:216-249 UniProt: 203-262       Transcript 1 (2)
                 3ex7 D 172 DDEDRKNPAYIPRKGLFFEHDLR---------------------GRWEHDKFREDEQAPKSRQELIALYGYDIRSAHN 249
                                   181       191  |      -         -    |  221       231       241        
                                                194                   216

Chain E from PDB  Type:PROTEIN  Length:142
 aligned with MGN_HUMAN | P61326 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:142
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  
            MGN_HUMAN     5 FYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
               SCOP domains d3ex7e_ E: Mago nashi protein                                                                                                                  SCOP domains
               CATH domains 3ex7E00 E:5-146 Mago nashi protein                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeeeee....eeeeeee.hhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 3 (1) Exon 3.1a  PDB: E:5-30    -------------------Exon 3.3b  PDB: E:50-86              Exon 3.4  PDB: E:87-114     -------------------------------- Transcript 3 (1)
           Transcript 3 (2) -------------------------Exon 3.2            ----------------------------------------------------------------Exon 3.5c  PDB: E:114-146         Transcript 3 (2)
                 3ex7 E   5 FYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144

Chain F from PDB  Type:RNA  Length:6
                                      
                 3ex7 F   1 UUUUUU   6

Chain G from PDB  Type:PROTEIN  Length:91
 aligned with RBM8A_HUMAN | Q9Y5S9 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:91
                                    73        83        93       103       113       123       133       143       153 
          RBM8A_HUMAN    64 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ex7G00 G:64-154  [code=3.30.70.330, no name defined]                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee......hhhhhhhhhhh...eeeee............eeeeee.hhhhhhhhhhhhh.........eeee.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------RRM  PDB: G:73-151 UniProt: 73-151                                             --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 3ex7 G  64 PGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
                                    73        83        93       103       113       123       133       143       153

Chain H from PDB  Type:PROTEIN  Length:392
 aligned with IF4A3_HUMAN | P38919 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                               411  
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
          IF4A3_HUMAN    22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhhh.....eeeee....hhhhhhhhhhh....eee...........eeeeeee....hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee..............eeee.....hhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhh..eee...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------Q_MOTIF  PDB: H:38-66        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1  PDB: H:22-57 UniProt: 1-57-----------------------Exon 2.3  PDB: H:81-103Exon 2.4             Exon 2.5  PDB: H:125-169 UniProt: 125-169    --------------------------Exon 2.7  PDB: H:196-243 UniProt: 196-243       ------------------------------------------------------------------------------------Exon 2.10  PDB: H:328-364            ------------------------------------------2.12 -- Transcript 2 (1)
           Transcript 2 (2) -----------------------------------Exon 2.2  PDB: H:57-81   ---------------------------------------------------------------------------------------Exon 2.6  PDB: H:169-196    ----------------------------------------------Exon 2.8  PDB: H:243-289 UniProt: 243-289      Exon 2.9  PDB: H:290-328               -----------------------------------Exon 2.11  PDB: H:364-407 UniProt: 364-407  ------ Transcript 2 (2)
                 3ex7 H  22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLILE 413
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411

Chain I from PDB  Type:PROTEIN  Length:62
 aligned with CASC3_HUMAN | O15234 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:83
                                   176       186       196       206       216       226       236       246   
          CASC3_HUMAN   167 PKHLDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAHN 249
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh...................---------------------.........hhhhh..hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: I:167-194 [INCOMPLETE]---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.6  PDB: I:216-249 UniProt: 203-262       Transcript 1 (2)
                 3ex7 I 167 PKHLDDDEDRKNPAYIPRKGLFFEHDLR---------------------GRWEHDKFREDEQAPKSRQELIALYGYDIRSAHN 249
                                   176       186       | -         -       216       226       236       246   
                                                     194                   216

Chain J from PDB  Type:RNA  Length:6
                                      
                 3ex7 J   1 UUUUUU   6

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Mago nashi protein (8)

Superfamily: Mago nashi protein (8)

Family: Mago nashi protein (8)

Protein domain: Mago nashi protein (8)

Human (Homo sapiens) [TaxId: 9606] (5)

1a	d3ex7a_	A:
1b	d3ex7e_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.330, no name defined] (307)

Human (Homo sapiens) (81)

1a	3ex7G00	G:64-154
1b	3ex7B00	B:64-157

Topology: Mago nashi protein (10)

Homologous Superfamily: Mago nashi protein (10)

Human (Homo sapiens) (5)

2a	3ex7E00	E:5-146
2b	3ex7A00	A:3-146

(no "Pfam Domain" information available for 3EX7)

Asymmetric Unit(hide GO term definitions)

Chain A,E (MGN_HUMAN | P61326)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain B,G (RBM8A_HUMAN | Q9Y5S9)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0000381	regulation of alternative mRNA splicing, via spliceosome	Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain C,H (IF4A3_HUMAN | P38919)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0035613	RNA stem-loop binding	Interacting selectively and non-covalently with a stem-loop in an RNA molecule. An RNA stem-loop is a secondary RNA structure consisting of a double-stranded RNA (dsRNA) stem and a terminal loop.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003729	mRNA binding	Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008143	poly(A) binding	Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043021	ribonucleoprotein complex binding	Interacting selectively and non-covalently with any complex of RNA and protein.
	GO:0035368	selenocysteine insertion sequence binding	Interacting selectively and non-covalently with the selenocysteine insertion sequence (SECIS), a regulatory sequence within mRNA which directs incorporation of a selenocysteine at a stop codon (UGA) during translation.
biological process
	GO:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	GO:0010501	RNA secondary structure unwinding	The process in which a secondary structure of RNA are broken or 'melted'.
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0008306	associative learning	Learning by associating a stimulus (the cause) with a particular outcome (the effect).
	GO:1990416	cellular response to brain-derived neurotrophic factor stimulus	A process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a brain-derived neurotrophic factor stimulus.
	GO:0072715	cellular response to selenite ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a selenite ion stimulus.
	GO:0048701	embryonic cranial skeleton morphogenesis	The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
	GO:0035640	exploration behavior	The specific behavior of an organism in response to a novel environment or stimulus.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0090394	negative regulation of excitatory postsynaptic potential	Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1904570	negative regulation of selenocysteine incorporation	Any process that stops, prevents or reduces the frequency, rate or extent of selenocysteine incorporation.
	GO:1904574	negative regulation of selenocysteine insertion sequence binding	Any process that stops, prevents or reduces the frequency, rate or extent of selenocysteine insertion sequence binding.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:1902415	regulation of mRNA binding	Any process that modulates the frequency, rate or extent of mRNA binding.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
	GO:0016259	selenocysteine metabolic process	The chemical reactions and pathways involving selenocysteine, an essential component of glutathione peroxidase and some other proteins.
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0071013	catalytic step 2 spliceosome	A spliceosomal complex that contains three snRNPs, including U5, bound to a splicing intermediate in which the first catalytic cleavage of the 5' splice site has occurred. The precise subunit composition differs significantly from that of the catalytic step 1, or activated, spliceosome, and includes many proteins in addition to those found in the associated snRNPs.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0043025	neuronal cell body	The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005681	spliceosomal complex	Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

Chain D,I (CASC3_HUMAN | O15234)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0006405	RNA export from nucleus	The directed movement of RNA from the nucleus to the cytoplasm.
	GO:0016070	RNA metabolic process	The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:0008298	intracellular mRNA localization	Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
	GO:0031124	mRNA 3'-end processing	Any process involved in forming the mature 3' end of an mRNA molecule.
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0006369	termination of RNA polymerase II transcription	The process in which the synthesis of an RNA molecule by RNA polymerase II using a DNA template is completed.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0035145	exon-exon junction complex	A multi-subunit complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

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UniProtKB/Swiss-Prot
	CASC3_HUMAN \| O15234	:	2hyi 2j0q 2j0s 2j0u 2xb2
	IF4A3_HUMAN \| P38919	:	2hxy 2hyi 2j0q 2j0s 2j0u 2xb2 4c9b 5mqf
	MGN_HUMAN \| P61326	:	1p27 2hyi 2j0q 2j0s 2xb2
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2hxy	STRUCTURE OF APO-EIF4AIII
2hyi	EJC WITH ADPNP INSTEAD OF ADP-ALF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 2)

PROSITE Motifs (3, 6)

Exons (19, 38)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (62, 130)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File