Annotations: 4DGW

Crystal Structure of the SF3a splicing factor complex of U2 snRNP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Prp11-like	8046219	4004963	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Hsp20 chaperone-like	8093058	3001242	SCOP2 (2022-06-29)
B	SCOP2 Family	Prp21-like	8047359	4005605	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Prp21-like	8093059	3002671	SCOP2 (2022-06-29)
A	SCOP2 Family	Prp9-like	8046221	4004965	SCOP2 (2022-06-29)
A	SCOP2 Family	HkH motif-containing C2H2 finger	8047131	4003065	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Prp9-like	8046394	3002670	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-beta-alpha zinc fingers	8093057	3001077	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	SF3A2	e4dgwC1	A: alpha arrays	X: HSP20-like	H: Pre-mRNA-splicing factor PRP11 C-terminal domain	T: Pre-mRNA-splicing factor PRP11 C-terminal domain	F: SF3A2	ECOD (v295)
B	Surp	e4dgwB1	A: alpha arrays	X: HSP20-like	H: Surp module (SWAP domain)	T: Surp module (SWAP domain)	F: Surp	ECOD (v295)
A	Surp	e4dgwA1	A: alpha arrays	X: HSP20-like	H: Surp module (SWAP domain)	T: Surp module (SWAP domain)	F: Surp	ECOD (v295)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.40.2690	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B	1.10.10.790	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Surp module	CATH (4.3.0)
B	6.10.250.1320	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF16835	Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11) (SF3A2)	Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11)	SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ...	SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). with Prp21 wrapping around Prp11 [1].	Domain
B	PF12230	Pre-mRNA splicing factor PRP21 like protein (PRP21_like_P)	Pre-mRNA splicing factor PRP21 like protein	-	Family
B	PF01805	Surp module (Surp)	Surp module	This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding [1].	Domain
A	PF16837	Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9 (SF3A3)	Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9	SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp2 ...	SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). Prp9 and Prp21 were not thought to interact with each other but the alpha1 helix of Prp9 does make important contacts with the SURP2 domain of Prp21, thus the two do interact via a bidentate-binding mode. Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA [1].	Domain
A	PF16958	Pre-mRNA-splicing factor PRP9 N-terminus (PRP9_N)	Pre-mRNA-splicing factor PRP9 N-terminus	This is the N-terminal domain of pre-mRNA-splicing factor PRP9 [1].	Domain
A	PF12171	Zinc-finger double-stranded RNA-binding (zf-C2H2_jaz)	Zinc-finger double-stranded RNA-binding	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Pre-mRNA-splicing factor PRP11	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process U2-type prespliceosome assembly	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex U2 snRNP membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex U2 snRNP catalytic step 2 spliceosome catalytic complex spliceosomal complex U2-type spliceosomal complex prespliceosome U2-type prespliceosome
B	Pre-mRNA-splicing factor PRP21	RNA binding binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions U2-type prespliceosome assembly mRNA splicing, via spliceosome cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process mRNA cis splicing, via spliceosome	membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex U2 snRNP membrane-bounded organelle spliceosomal snRNP complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex Sm-like protein family complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex U2 snRNP U2-type spliceosomal complex prespliceosome U2-type prespliceosome spliceosomal complex catalytic step 2 spliceosome catalytic complex
A	Pre-mRNA-splicing factor PRP9	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA processing ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing protein-RNA complex assembly nucleobase-containing compound metabolic process RNA biosynthetic process cellular component organization cellular component biogenesis nucleic acid biosynthetic process spliceosomal complex assembly protein-RNA complex organization cellular component assembly protein-containing complex assembly RNA processing cellular component organization or biogenesis mRNA splice site recognition RNA splicing protein-containing complex organization primary metabolic process mRNA 5'-splice site recognition gene expression nucleobase-containing compound biosynthetic process mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process biosynthetic process RNA splicing, via transesterification reactions mRNA cis splicing, via spliceosome mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process U2-type prespliceosome assembly	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex U2-type spliceosomal complex prespliceosome U2-type prespliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR031781	SF3A2 domain	Domain
C	IPR003604	Matrin/U1-C-like, C2H2-type zinc finger	Domain
C	IPR013087	Zinc finger C2H2-type	Domain
C	IPR052092	Splicing Factor 3A Subunit 2	Family
C	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
B	IPR045146	Splicing factor 3A subunit 1	Family
B	IPR035967	SWAP/Surp superfamily	Homologous Superfamily
B	IPR000061	SWAP/Surp	Domain
B	IPR022030	Splicing factor 3A subunit 1, conserved domain	Domain
A	IPR003604	Matrin/U1-C-like, C2H2-type zinc finger	Domain
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A	IPR031590	Pre-mRNA-splicing factor Prp9, N-terminal	Domain
A	IPR031774	SF3A3 domain	Domain
A	IPR024598	Splicing factor SF3a60 /Prp9 subunit, C-terminal	Domain
A	IPR000690	Matrin/U1-C, C2H2-type zinc finger	Domain
A	IPR051421	RNA Processing and DNA Damage Response Regulator	Family
A	IPR022755	Zinc finger, double-stranded RNA binding	Domain

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.