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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE EXON JUNCTION COMPLEX AT 3.2 A RESOLUTION
 
Authors :  F. Bono, J. Ebert, E. Lorentzen, E. Conti
Date :  04 Aug 06  (Deposition) - 30 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,T
Biol. Unit 1:  A,C,D,E,T  (1x)
Biol. Unit 2:  B,F,G,H,I  (1x)
Keywords :  Hydrolase, Mrna Processing, Mrna Splicing, Mrna Transport, Nuclear Protein, Dead-Box Helicase, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Bono, J. Ebert, E. Lorentzen, E. Conti
The Crystal Structure Of The Exon Junction Complex Reveals How It Maintains A Stable Grip On Mrna.
Cell(Cambridge, Mass. ) V. 126 713 2006
PubMed-ID: 16923391  |  Reference-DOI: 10.1016/J.CELL.2006.08.006

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX48
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPETMCN
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEIF4AIII RNA-HELICASE, DEAD BOX PROTEIN 48, EUKARYOTIC INITIATION FACTOR 4A-LIKE NUK-34, HNMP 265, NUCLEAR MATRIX PROTEIN 265, EUKARYOTIC TRANSLATION INITIATION FACTOR 4A ISOFORM 3
 
Molecule 2 - PROTEIN MAGO NASHI HOMOLOG
    ChainsC, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPETMCN
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMGN
 
Molecule 3 - RNA-BINDING PROTEIN 8A
    ChainsD, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPETMCN
    Expression System Vector TypePLASMID
    FragmentRESIDUES 66-174
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymY14, RNA-BINDING MOTIF PROTEIN 8A, RIBONUCLEOPROTEIN RBM8A, RNA-BINDING PROTEIN Y14, BINDER OF OVCA1-1, BOV-1
 
Molecule 4 - PROTEIN CASC3
    ChainsT, I
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPETMCN
    Expression System Vector TypePLASMID
    FragmentRESIDUES 137-286
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBARENTSZ, CANCER SUSCEPTIBILITY CANDIDATE GENE 3 PROTEIN, METASTATIC LYMPH NODE PROTEIN 51 MLN 51 PROTEIN BARENTSZ PROTEIN, BTZ
 
Molecule 5 - 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
    ChainsE, H
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit ABCDEFGHIT
Biological Unit 1 (1x)A CDE    T
Biological Unit 2 (1x) B   FGHI 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:89 , ASP A:187 , GLU A:188 , GLY A:340 , ANP A:1413BINDING SITE FOR RESIDUE MG A1412
2AC2SOFTWARETHR B:89 , ASP B:187 , GLU B:188 , ANP B:1413BINDING SITE FOR RESIDUE MG B1412
3AC3SOFTWAREPHE A:58 , LYS A:60 , GLN A:65 , SER A:84 , GLY A:85 , GLY A:87 , LYS A:88 , THR A:89 , ALA A:90 , GLU A:188 , GLY A:340 , ASP A:342 , ARG A:367 , ARG A:370 , TYR A:371 , MG A:1412BINDING SITE FOR RESIDUE ANP A1413
4AC4SOFTWAREPHE B:58 , LYS B:60 , GLN B:65 , SER B:84 , GLY B:85 , THR B:86 , GLY B:87 , LYS B:88 , THR B:89 , ALA B:90 , GLU B:188 , GLY B:340 , ASP B:342 , ARG B:367 , ARG B:370 , TYR B:371 , MG B:1412BINDING SITE FOR RESIDUE ANP B1413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J0Q)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Thr A:107 -Gln A:108
2Gly I:216 -Arg I:217
3Tyr I:240 -Gly I:241
4Ser I:246 -Ala I:247
5Glu T:215 -Gly T:216
6Gly T:216 -Arg T:217
7Tyr T:240 -Gly T:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071090D270GIF4A3_HUMANDisease (RCPS)587777204A/BD270G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071090D270GIF4A3_HUMANDisease (RCPS)587777204AD270G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071090D270GIF4A3_HUMANDisease (RCPS)587777204BD270G

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.IF4A3_HUMAN38-66
 
  2A:38-66
B:38-66
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM8A_HUMAN73-151
 
  2D:73-151
G:73-151
3DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.IF4A3_HUMAN185-193
 
  2A:185-193
B:185-193
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.IF4A3_HUMAN38-66
 
  1A:38-66
-
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM8A_HUMAN73-151
 
  1D:73-151
-
3DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.IF4A3_HUMAN185-193
 
  1A:185-193
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.IF4A3_HUMAN38-66
 
  1-
B:38-66
2RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.RBM8A_HUMAN73-151
 
  1-
G:73-151
3DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.IF4A3_HUMAN185-193
 
  1-
B:185-193

(-) Exons   (19, 38)

Asymmetric Unit (19, 38)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002646451aENSE00001517546chr17:38296507-38297032526CASC3_HUMAN1-77770--
1.2ENST000002646452ENSE00000720185chr17:38297460-3829748728CASC3_HUMAN78-87100--
1.3ENST000002646453ENSE00001120433chr17:38297823-3829786038CASC3_HUMAN87-99130--
1.4aENST000002646454aENSE00000863354chr17:38318006-38318164159CASC3_HUMAN100-152530--
1.5ENST000002646455ENSE00000863355chr17:38318255-38318406152CASC3_HUMAN153-203512I:168-196
T:168-197
29
30
1.6ENST000002646456ENSE00000863356chr17:38318978-38319154177CASC3_HUMAN203-262602I:215-248
T:214-248
34
35
1.7bENST000002646457bENSE00000863357chr17:38319734-38320419686CASC3_HUMAN262-4912300--
1.8bENST000002646458bENSE00000863358chr17:38323050-3832311465CASC3_HUMAN491-512220--
1.9ENST000002646459ENSE00000900529chr17:38323751-38323865115CASC3_HUMAN513-551390--
1.10ENST0000026464510ENSE00000950687chr17:38324103-3832420199CASC3_HUMAN551-584340--
1.11bENST0000026464511bENSE00000900527chr17:38324456-38324670215CASC3_HUMAN584-655720--
1.12ENST0000026464512ENSE00001322421chr17:38325577-38325699123CASC3_HUMAN656-696410--
1.13aENST0000026464513aENSE00001350371chr17:38325851-3832591565CASC3_HUMAN697-70370--
1.13cENST0000026464513cENSE00001350362chr17:38326700-383284311732CASC3_HUMAN-00--

2.1ENST000002693491ENSE00001213025chr17:78120938-78120592347IF4A3_HUMAN1-57572A:22-57
B:22-57
36
36
2.2ENST000002693492ENSE00000949585chr17:78118043-7811797173IF4A3_HUMAN57-81252A:57-81
B:57-81
25
25
2.3ENST000002693493ENSE00000949586chr17:78115647-7811558167IF4A3_HUMAN81-103232A:81-103
B:81-103
23
23
2.4ENST000002693494ENSE00000949587chr17:78115180-7811511863IF4A3_HUMAN104-124212A:104-124
B:104-124
21
21
2.5ENST000002693495ENSE00001303885chr17:78113939-78113807133IF4A3_HUMAN125-169452A:125-169
B:125-169
45
45
2.6ENST000002693496ENSE00000949589chr17:78113549-7811346981IF4A3_HUMAN169-196282A:169-196
B:169-196
28
28
2.7ENST000002693497ENSE00000949591chr17:78112961-78112820142IF4A3_HUMAN196-243482A:196-243
B:196-243
48
48
2.8ENST000002693498ENSE00001212947chr17:78112079-78111941139IF4A3_HUMAN243-289472A:243-289
B:243-289
47
47
2.9ENST000002693499ENSE00001212937chr17:78111300-78111185116IF4A3_HUMAN290-328392A:290-328
B:290-328
39
39
2.10ENST0000026934910ENSE00000949595chr17:78110134-78110027108IF4A3_HUMAN328-364372A:328-364
B:328-364
37
37
2.11ENST0000026934911ENSE00001213013chr17:78109930-78109803128IF4A3_HUMAN364-407442A:364-407
B:364-407
44
44
2.12ENST0000026934912ENSE00001318045chr17:78109305-78109019287IF4A3_HUMAN407-41152A:407-411
B:407-411
5
5

3.1aENST000003714701aENSE00001853117chr1:53704282-53704033250MGN_HUMAN1-30302C:4-30
F:4-30
27
27
3.2ENST000003714702ENSE00001735272chr1:53701307-5370124959MGN_HUMAN30-49202C:30-49
F:30-49
20
20
3.3bENST000003714703bENSE00001689792chr1:53699324-53699214111MGN_HUMAN50-86372C:50-86
F:50-86
37
37
3.4ENST000003714704ENSE00001064642chr1:53694626-5369454483MGN_HUMAN87-114282C:87-114
F:87-114
28
28
3.5cENST000003714705cENSE00001064645chr1:53692816-53692564253MGN_HUMAN114-146332C:114-146
F:114-146
33
33

(-) Sequences/Alignments

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:390
 aligned with IF4A3_HUMAN | P38919 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:390
                                    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 411
               SCOP domains d2j0qa1 A:22-243 Probable ATP-dependent RNA helicase DDX48                                                                                                                                                                    d2j0qa2 A:244-411 Probable ATP-dependent RNA helicase DDX48                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.......eeeeeeehhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhhhh....eee..hhhhh....eeeeeee....hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee.hhhh.......eeeeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh....ee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------Q_MOTIF  PDB: A:38-66        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1  PDB: A:22-57 UniProt: 1-57-----------------------Exon 2.3  PDB: A:81-103Exon 2.4             Exon 2.5  PDB: A:125-169 UniProt: 125-169    --------------------------Exon 2.7  PDB: A:196-243 UniProt: 196-243       ------------------------------------------------------------------------------------Exon 2.10  PDB: A:328-364            ------------------------------------------2.12  Transcript 2 (1)
           Transcript 2 (2) -----------------------------------Exon 2.2  PDB: A:57-81   ---------------------------------------------------------------------------------------Exon 2.6  PDB: A:169-196    ----------------------------------------------Exon 2.8  PDB: A:243-289 UniProt: 243-289      Exon 2.9  PDB: A:290-328               -----------------------------------Exon 2.11  PDB: A:364-407 UniProt: 364-407  ---- Transcript 2 (2)
                 2j0q A  22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 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

Chain B from PDB  Type:PROTEIN  Length:390
 aligned with IF4A3_HUMAN | P38919 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:390
                                    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 411
               SCOP domains d2j0qb1 B:22-243 Probable ATP-dependent RNA helicase DDX48                                                                                                                                                                    d2j0qb2 B:244-411 Probable ATP-dependent RNA helicase DDX48                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh.............hhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhh.........eeeeehhhhhh...hhhhhhhhhhhh....eeeeee...hhhhhhhhhhh....eee...........eeeeeee....hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....eeee.hhhh.......eeeeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhh....ee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------Q_MOTIF  PDB: B:38-66        ----------------------------------------------------------------------------------------------------------------------DEAD_ATP_-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.1  PDB: B:22-57 UniProt: 1-57-----------------------Exon 2.3  PDB: B:81-103Exon 2.4             Exon 2.5  PDB: B:125-169 UniProt: 125-169    --------------------------Exon 2.7  PDB: B:196-243 UniProt: 196-243       ------------------------------------------------------------------------------------Exon 2.10  PDB: B:328-364            ------------------------------------------2.12  Transcript 2 (1)
           Transcript 2 (2) -----------------------------------Exon 2.2  PDB: B:57-81   ---------------------------------------------------------------------------------------Exon 2.6  PDB: B:169-196    ----------------------------------------------Exon 2.8  PDB: B:243-289 UniProt: 243-289      Exon 2.9  PDB: B:290-328               -----------------------------------Exon 2.11  PDB: B:364-407 UniProt: 364-407  ---- Transcript 2 (2)
                 2j0q B  22 DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILAPTRELAVQIQKGLLALGDYMNVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTLEGIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVDWLTEKMREANFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVWARGLDVPQVSLIINYDLPNNRELYIHRIGRSGRYGRKGVAINFVKNDDIRILRDIEQYYSTQIDEMPMNVADLI 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

Chain C from PDB  Type:PROTEIN  Length:143
 aligned with MGN_HUMAN | P61326 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143   
            MGN_HUMAN     4 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
               SCOP domains d2j0qc1 C:4-145 Mago nashi protein                                                                                                            - SCOP domains
               CATH domains 2j0qC00 C:4-146 Mago nashi protein                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeeeeee...eeeeeee.hhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhh............eeeeeeee....eeeeee...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 3 (1) Exon 3.1a  PDB: C:4-30     -------------------Exon 3.3b  PDB: C:50-86              Exon 3.4  PDB: C:87-114     -------------------------------- Transcript 3 (1)
           Transcript 3 (2) --------------------------Exon 3.2            ----------------------------------------------------------------Exon 3.5c  PDB: C:114-146         Transcript 3 (2)
                 2j0q C   4 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143   

Chain D from PDB  Type:PROTEIN  Length:89
 aligned with RBM8A_HUMAN | Q9Y5S9 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:89
                                    75        85        95       105       115       125       135       145         
          RBM8A_HUMAN    66 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
               SCOP domains d2j0qd1 D:66-154 RNA-binding protein 8                                                    SCOP domains
               CATH domains 2j0qD00 D:66-154  [code=3.30.70.330, no name defined]                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhh.....eee............eeeeee.hhhhhhhhhhhhh.........eeee.ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RRM  PDB: D:73-151 UniProt: 73-151                                             --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2j0q D  66 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
                                    75        85        95       105       115       125       135       145         

Chain E from PDB  Type:RNA  Length:6
                                      
                 2j0q E   1 UUUUUU   6

Chain F from PDB  Type:PROTEIN  Length:143
 aligned with MGN_HUMAN | P61326 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:143
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143   
            MGN_HUMAN     4 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
               SCOP domains d2j0qf1 F:4-145 Mago nashi protein                                                                                                            - SCOP domains
               CATH domains 2j0qF00 F:4-146 Mago nashi protein                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee..eeeeeeeeee...eeeeeee.hhhhh..eeeeeeehhhhhhhhhhhhhhhhhhhh............eeeeeeee..eeeeeeee...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 3 (1) Exon 3.1a  PDB: F:4-30     -------------------Exon 3.3b  PDB: F:50-86              Exon 3.4  PDB: F:87-114     -------------------------------- Transcript 3 (1)
           Transcript 3 (2) --------------------------Exon 3.2            ----------------------------------------------------------------Exon 3.5c  PDB: F:114-146         Transcript 3 (2)
                 2j0q F   4 DFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKPI 146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143   

Chain G from PDB  Type:PROTEIN  Length:89
 aligned with RBM8A_HUMAN | Q9Y5S9 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:89
                                    75        85        95       105       115       125       135       145         
          RBM8A_HUMAN    66 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
               SCOP domains d2j0qg1 G:66-154 RNA-binding protein 8                                                    SCOP domains
               CATH domains 2j0qG00 G:66-154  [code=3.30.70.330, no name defined]                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhh.....eee............eeeeee.hhhhhhhhhhhhh.........eeee.ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------RRM  PDB: G:73-151 UniProt: 73-151                                             --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 2j0q G  66 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRGP 154
                                    75        85        95       105       115       125       135       145         

Chain H from PDB  Type:RNA  Length:6
                                      
                 2j0q H   1 UUUUUU   6

Chain I from PDB  Type:PROTEIN  Length:63
 aligned with CASC3_HUMAN | O15234 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:81
                                   177       187       197       207       217       227       237       247 
          CASC3_HUMAN   168 KHLDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAH 248
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh.....................------------------.........hhhhhh..hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: I:168-196            --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.6  PDB: I:215-248 UniProt: 203-262      Transcript 1 (2)
                 2j0q I 168 KHLDDDEDRKNPAYIPRKGLFFEHDLRGQ------------------EGRWEHDKFREDEQAPKSRQELIALYGYDIRSAH 248
                                   177       187        |-         -       217       227       237       247 
                                                      196                215                                 

Chain T from PDB  Type:PROTEIN  Length:65
 aligned with CASC3_HUMAN | O15234 from UniProtKB/Swiss-Prot  Length:703

    Alignment length:81
                                   177       187       197       207       217       227       237       247 
          CASC3_HUMAN   168 KHLDDDEDRKNPAYIPRKGLFFEHDLRGQTQEEEVRPKGRQRKLWKDEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAH 248
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............................----------------..........hhhhh...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: T:168-197            --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------Exon 1.6  PDB: T:214-248 UniProt: 203-262      Transcript 1 (2)
                 2j0q T 168 KHLDDDEDRKNPAYIPRKGLFFEHDLRGQT----------------DEGRWEHDKFREDEQAPKSRQELIALYGYDIRSAH 248
                                   177       187       197         -      |217       227       237       247 
                                                       197              214                                  

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 8)

Asymmetric Unit

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J0Q)

(-) Gene Ontology  (62, 130)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 C,F   (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 D,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 I,T   (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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        CASC3_HUMAN | O152342hyi 2j0s 2j0u 2xb2 3ex7
        IF4A3_HUMAN | P389192hxy 2hyi 2j0s 2j0u 2xb2 3ex7 4c9b 5mqf
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(-) Related Entries Specified in the PDB File

1p27 CRYSTAL STRUCTURE OF THE HUMAN Y14/MAGOH COMPLEX
2j0s THE CRYSTAL STRUCTURE OF THE EXON JUNCTION COMPLEX AT 2.2 A RESOLUTION RELATED ENTRIES
2j0u THE CRYSTAL STRUCTURE OF EIF4AIII-BARENTSZ COMPLEX AT 3.0 A RESOLUTION