2OZB - 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 :   STRUCTURE OF A HUMAN PRP31-15.5K-U4 SNRNA COMPLEX

Authors :   S. Liu, R. Luehrmann, M. C. Wahl

Date :   26 Feb 07 (Deposition) - 20 Mar 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Rna-Protein Complex, Ribonucleoprotein Particle (Rnp), Pre-Mrna Splicing, U4/U6 Di-Snrna, U4/U6 Di-Snrnp, Hierarchical Assembly, Nop Domain, Rnp-Binding Domain, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Liu, P. Li, O. Dybkov, S. Nottrott, K. Hartmuth, R. Luhrmann, T. Carlomagno, M. C. Wahl
Binding Of The Human Prp31 Nop Domain To A Composite Rna-Protein Platform In U4 Snrnp.
Science V. 316 115 2007
PubMed-ID: 17412961 | Reference-DOI: 10.1126/SCIENCE.1137924

Molecule 1 - RNA COMPRISING THE 5' STEM-LOOP RNA OF U4SNRNA
	Chains	:	C, F
	Engineered	:	YES
	Fragment	:	U4 5'-SL, RESIDUES 20-52
	Other Details	:	RNA WAS CHEMICALLY SYNTHESIZED ACCORDING TO GENE RNU4A (RESIDUES 20-52)
	Synthetic	:	YES

Molecule 2 - U4/U6.U5 TRI-SNRNP 15.5 KDA PROTEIN
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-4T-2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	NHP2L1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	HELA CELLS
	Synonym	:	HIGH MOBILITY GROUP-LIKE NUCLEAR PROTEIN 2 HOMOLOG 1, NHP2- LIKE PROTEIN 1, OTK27, HSNU13

Molecule 3 - U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP31
	Chains	:	B, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PRP31, RESIDUES 78-333
	Gene	:	PRPF31, PRP31
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Strain	:	HELA CELLS
	Synonym	:	PRE-MRNA-PROCESSING FACTOR 31, U4/U6 SNRNP 61 KDA PROTEIN, HPRP31, PROTEIN 61K, SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY- BR-99

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:77 , GLU A:124 , HOH A:518 , HOH A:519	BINDING SITE FOR RESIDUE CA A 503
2	AC2	SOFTWARE	HOH B:559 , HOH B:560 , HOH B:562 , HOH B:563 , HOH B:564	BINDING SITE FOR RESIDUE CA B 502
3	AC3	SOFTWARE	HOH B:503 , ASP E:322 , HOH E:502 , HOH E:503 , HOH E:504 , HOH E:505 , HOH E:506	BINDING SITE FOR RESIDUE CA E 501

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

Asymmetric Unit

No.	Residues
1	Glu A:3	-	Ala A:4
2	Asp A:5	-	Val A:6
3	Tyr A:11	-	Pro A:12
4	Glu A:61	-	Pro A:62
5	Tyr D:11	-	Pro D:12
6	Glu D:61	-	Pro D:62
7	Gly E:176	-	Gln E:177

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034155	T	19	N	NH2L1_HUMAN	Polymorphism	1802521	A/D	T	19	N
2	UniProt	VAR_025630	A	194	E	PRP31_HUMAN	Disease (RP11)	119475043	B/E	A	194	E
3	UniProt	VAR_025631	A	216	P	PRP31_HUMAN	Disease (RP11)	119475042	B/E	A	216	P

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034155	T	19	N	NH2L1_HUMAN	Polymorphism	1802521	A	T	19	N
2	UniProt	VAR_025630	A	194	E	PRP31_HUMAN	Disease (RP11)	119475043	B	A	194	E
3	UniProt	VAR_025631	A	216	P	PRP31_HUMAN	Disease (RP11)	119475042	B	A	216	P

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

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_034155	T	19	N	NH2L1_HUMAN	Polymorphism	1802521	D	T	19	N
2	UniProt	VAR_025630	A	194	E	PRP31_HUMAN	Disease (RP11)	119475043	E	A	194	E
3	UniProt	VAR_025631	A	216	P	PRP31_HUMAN	Disease (RP11)	119475042	E	A	216	P

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	NH2L1_HUMAN	73-90	2	A:73-90 D:73-90
2	NOP	PS51358	Nop domain profile.	PRP31_HUMAN	215-333	2	B:215-333 E:215-333

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	NH2L1_HUMAN	73-90	1	A:73-90 -
2	NOP	PS51358	Nop domain profile.	PRP31_HUMAN	215-333	1	B:215-333 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	NH2L1_HUMAN	73-90	1	- D:73-90
2	NOP	PS51358	Nop domain profile.	PRP31_HUMAN	215-333	1	- E:215-333

Asymmetric Unit (9, 18)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000321030	1a	ENSE00001357861	chr19:54618837-54619177	341	PRP31_HUMAN	-	0	0	-	-
1.3c	ENST00000321030	3c	ENSE00000856128	chr19:54621651-54621835	185	PRP31_HUMAN	1-59	59	0	-	-
1.4a	ENST00000321030	4a	ENSE00000725537	chr19:54621953-54622013	61	PRP31_HUMAN	60-80	21	0	-	-
1.5	ENST00000321030	5	ENSE00001122691	chr19:54625239-54625322	84	PRP31_HUMAN	80-108	29	2	B:85-108 E:85-108	24 24
1.6	ENST00000321030	6	ENSE00000725528	chr19:54625876-54625973	98	PRP31_HUMAN	108-140	33	2	B:108-140 E:108-140	33 33
1.7	ENST00000321030	7	ENSE00000725522	chr19:54626833-54626939	107	PRP31_HUMAN	141-176	36	2	B:141-176 E:141-176	36 36
1.8	ENST00000321030	8	ENSE00000954003	chr19:54627128-54627297	170	PRP31_HUMAN	176-233	58	2	B:176-233 E:176-233	58 58
1.9d	ENST00000321030	9d	ENSE00000954004	chr19:54627878-54628035	158	PRP31_HUMAN	233-285	53	2	B:233-285 (gaps) E:233-285 (gaps)	53 53
1.10b	ENST00000321030	10b	ENSE00000725505	chr19:54629903-54629992	90	PRP31_HUMAN	286-315	30	2	B:286-315 E:286-315	30 30
1.11c	ENST00000321030	11c	ENSE00001281426	chr19:54631448-54631575	128	PRP31_HUMAN	316-358	43	2	B:316-333 E:316-333	18 18
1.11f	ENST00000321030	11f	ENSE00000954006	chr19:54631680-54631752	73	PRP31_HUMAN	358-382	25	0	-	-
1.12b	ENST00000321030	12b	ENSE00001281305	chr19:54632432-54632560	129	PRP31_HUMAN	383-425	43	0	-	-
1.12e	ENST00000321030	12e	ENSE00001675411	chr19:54632647-54632745	99	PRP31_HUMAN	426-458	33	0	-	-
1.13a	ENST00000321030	13a	ENSE00001629454	chr19:54634738-54635140	403	PRP31_HUMAN	459-499	41	0	-	-

2.2a	ENST00000355257	2a	ENSE00001488410	chr22:42084913-42084798	116	NH2L1_HUMAN	1-1	1	0	-	-
2.6b	ENST00000355257	6b	ENSE00000656116	chr22:42076368-42076248	121	NH2L1_HUMAN	2-42	41	2	A:3-42 D:4-42	40 39
2.7e	ENST00000355257	7e	ENSE00001948112	chr22:42071199-42069934	1266	NH2L1_HUMAN	42-128	87	2	A:42-128 D:42-128	87 87

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:126
 aligned with NH2L1_HUMAN | P55769 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:126
                                    12        22        32        42        52        62        72        82        92       102       112       122      
          NH2L1_HUMAN     3 EADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
               SCOP domains -d2ozba1 A:4-128 Spliceosomal 15.5kd protein                                                                                   SCOP domains
               CATH domains 2ozbA00 A:3-128  [code=3.30.1330.30, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeee......hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------N------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------RIBOSOMAL_L7AE    -------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.6b  PDB: A:3-42 UniProt: 2-42    -------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------Exon 2.7e  PDB: A:42-128 UniProt: 42-128                                                Transcript 2 (2)
                 2ozb A   3 EADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with PRP31_HUMAN | Q8WWY3 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:249
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324         
          PRP31_HUMAN    85 EAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQE 333
               SCOP domains d2ozbb1 B:85-333 U4/U6 small nuclear ribonucleoprotein Prp31                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhh.hhhhh....hhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....----------...........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------E---------------------P--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------NOP  PDB: B:215-333 UniProt: 215-333                                                                                    PROSITE
           Transcript 1 (1) Exon 1.5  PDB: B:85-108 --------------------------------Exon 1.7  PDB: B:141-176            --------------------------------------------------------Exon 1.9d  PDB: B:233-285 (gaps) UniProt: 233-285    Exon 1.10b  PDB: B:286-315    Exon 1.11c         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.6  PDB: B:108-140         -----------------------------------Exon 1.8  PDB: B:176-233 UniProt: 176-233                 ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ozb B  85 EAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQ----------SVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQE 333
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254|        - |     274       284       294       304       314       324         
                                                                                                                                                                                                    255        266

Chain C from PDB  Type:RNA  Length:33
                                                                 
                 2ozb C  20 AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU  52
                                    29        39        49

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with NH2L1_HUMAN | P55769 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:125
                                    13        23        33        43        53        63        73        83        93       103       113       123     
          NH2L1_HUMAN     4 ADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
               SCOP domains d2ozbd1 D:4-128 Spliceosomal 15.5kd protein                                                                                   SCOP domains
               CATH domains 2ozbD00 D:4-128  [code=3.30.1330.30, no name defined]                                                                         CATH domains
           Pfam domains (1) ----------------Ribosomal_L7Ae-2ozbD01 D:20-114                                                                -------------- Pfam domains (1)
           Pfam domains (2) ----------------Ribosomal_L7Ae-2ozbD02 D:20-114                                                                -------------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeee......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------N------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------RIBOSOMAL_L7AE    -------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.6b  PDB: D:4-42 UniProt: 2-42   -------------------------------------------------------------------------------------- Transcript 2 (1)
           Transcript 2 (2) --------------------------------------Exon 2.7e  PDB: D:42-128 UniProt: 42-128                                                Transcript 2 (2)
                 2ozb D   4 ADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV 128
                                    13        23        33        43        53        63        73        83        93       103       113       123

Chain E from PDB  Type:PROTEIN  Length:240
 aligned with PRP31_HUMAN | Q8WWY3 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:249
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324         
          PRP31_HUMAN    85 EAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQE 333
               SCOP domains d2ozbe_ E: U4/U6 small nuclear ribonucleoprotein Prp31                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------NOSIC-2ozbE01 E:92-144                               -----------------------------------------Nop-2ozbE03 E:186-333                                                                                                                                Pfam domains (1)
           Pfam domains (2) -------NOSIC-2ozbE02 E:92-144                               -----------------------------------------Nop-2ozbE04 E:186-333                                                                                                                                Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......---------...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------E---------------------P--------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------NOP  PDB: E:215-333 UniProt: 215-333                                                                                    PROSITE
           Transcript 1 (1) Exon 1.5  PDB: E:85-108 --------------------------------Exon 1.7  PDB: E:141-176            --------------------------------------------------------Exon 1.9d  PDB: E:233-285 (gaps) UniProt: 233-285    Exon 1.10b  PDB: E:286-315    Exon 1.11c         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.6  PDB: E:108-140         -----------------------------------Exon 1.8  PDB: E:176-233 UniProt: 176-233                 ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2ozb E  85 EAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQR---------SVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQE 333
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 |       - |     274       284       294       304       314       324         
                                                                                                                                                                                                     256       266

Chain F from PDB  Type:RNA  Length:33
                                                                 
                 2ozb F  20 AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU  52
                                    29        39        49

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: All alpha proteins (14657)

Fold: Nop domain (3)

Superfamily: Nop domain (3)

Family: Nop domain (2)

Protein domain: U4/U6 small nuclear ribonucleoprotein Prp31 (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d2ozbb1	B:85-333
1b	d2ozbe_	E:

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

Fold: Bacillus chorismate mutase-like (324)

Superfamily: L30e-like (93)

Family: L30e/L7ae ribosomal proteins (84)

Protein domain: Spliceosomal 15.5kd protein (3)

Human (Homo sapiens) [TaxId: 9606] (3)

2a	d2ozba1	A:4-128
2b	d2ozbd1	D:4-128

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.30, no name defined] (102)

[unclassified] (5)

1a	2ozbD00	D:4-128
1b	2ozbA00	A:3-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: RNA_ribose_bind (78)

Family: Ribosomal_L7Ae (69)

Homo sapiens (Human) (4)

1a	Ribosomal_L7Ae-2ozbD01	D:20-114
1b	Ribosomal_L7Ae-2ozbD02	D:20-114

Clan: no clan defined [family: NOSIC] (4)

Family: NOSIC (4)

Homo sapiens (Human) (1)

2a	NOSIC-2ozbE01	E:92-144
2b	NOSIC-2ozbE02	E:92-144

Clan: no clan defined [family: Nop] (5)

Family: Nop (5)

Homo sapiens (Human) (1)

3a	Nop-2ozbE03	E:186-333
3b	Nop-2ozbE04	E:186-333

Asymmetric Unit(hide GO term definitions)

Chain A,D (NH2L1_HUMAN | P55769)

molecular function
	GO:0051117	ATPase binding	Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0034511	U3 snoRNA binding	Interacting selectively and non-covalently with U3 small nucleolar RNA.
	GO:0030621	U4 snRNA binding	Interacting selectively and non-covalently with the U4 small nuclear RNA (U4 snRNA).
	GO:0030622	U4atac snRNA binding	Interacting selectively and non-covalently with the U4atac small nuclear RNA (U4atac snRNA).
	GO:0034512	box C/D snoRNA binding	Interacting selectively and non-covalently with box C/D small nucleolar RNA.
	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:0030515	snoRNA binding	Interacting selectively and non-covalently with small nucleolar RNA.
biological process
	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: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:0000470	maturation of LSU-rRNA	Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule.
	GO:0030490	maturation of SSU-rRNA	Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule.
	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:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0046540	U4/U6 x U5 tri-snRNP complex	A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
	GO:0031428	box C/D snoRNP complex	A ribonucleoprotein complex containing small nucleolar RNA of the box C/D type that can carry out ribose-2'-O-methylation of target RNAs.
	GO:0022625	cytosolic large ribosomal subunit	The large subunit of a ribosome located in the cytosol.
	GO:0001651	dense fibrillar component	A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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:0071011	precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0032040	small-subunit processome	A large ribonucleoprotein complex that is an early preribosomal complex. In S. cerevisiae, it has a size of 80S and consists of the 35S pre-rRNA, early-associating ribosomal proteins most of which are part of the small ribosomal subunit, the U3 snoRNA and associated proteins.
	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,E (PRP31_HUMAN | Q8WWY3)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0030621	U4 snRNA binding	Interacting selectively and non-covalently with the U4 small nuclear RNA (U4 snRNA).
	GO:0030622	U4atac snRNA binding	Interacting selectively and non-covalently with the U4atac small nuclear RNA (U4atac snRNA).
	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:0070990	snRNP binding	Interacting selectively and non-covalently with any part of a small nuclear ribonucleoprotein particle.
biological process
	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: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:0071166	ribonucleoprotein complex localization	Any process in which a ribonucleoprotein complex is transported to, or maintained in, a specific location within a cell.
	GO:0048254	snoRNA localization	Any process in which small nucleolar RNA is transported to, or maintained in, a specific location.
	GO:0000244	spliceosomal tri-snRNP complex assembly	The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex.
cellular component
	GO:0015030	Cajal body	A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
	GO:0071339	MLL1 complex	A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
	GO:0005684	U2-type spliceosomal complex	Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.
	GO:0005687	U4 snRNP	A ribonucleoprotein complex that contains small nuclear RNA U4.
	GO:0046540	U4/U6 x U5 tri-snRNP complex	A ribonucleoprotein complex formed by the association of the U4/U6 and U5 small nuclear ribonucleoproteins.
	GO:0005690	U4atac snRNP	A ribonucleoprotein complex that contains small nuclear RNA U4atac.
	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:0071011	precatalytic spliceosome	A spliceosomal complex that is formed by the recruitment of a preassembled U5-containing tri-snRNP to the prespliceosome. Although all 5 snRNPs are present, the precatalytic spliceosome is catalytically inactive. The precatalytic spliceosome includes many proteins in addition to those found in the associated snRNPs.
	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.

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	PRP31_HUMAN \| Q8WWY3
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	NH2L1_HUMAN \| P55769	:	1e7k 2jnb 3jcr 3siu 3siv
	PRP31_HUMAN \| Q8WWY3	:	3jcr 3siu 3siv

1e7k	BINARY 15.5-RNA COMPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (2, 4)

Exons (9, 18)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (1, 2)

Pfam Domains (3, 6)

Gene Ontology (39, 52)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File