4WAN | pdb_00004wan

Crystal structure of Msl5 protein in complex with RNA at 1.8 A

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)
G	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8085086	3001023	SCOP2B (2022-06-29)
E	SCOP2 Family	Eukaryotic type KH-domain (KH-domain type I)	8085085	4001190	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8085086	3001023	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8085086	3001023	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8085086	3001023	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	KH_1_2	e4wanG1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)
E	KH_1_2	e4wanE1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)
C	KH_1_2	e4wanC1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)
A	KH_1_2	e4wanA1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_1_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
E	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
A	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF22675	KHDC4/BBP-like, KH-domain type I (KH-I_KHDC4-BBP)	KHDC4/BBP-like, KH-domain type I	This entry represents eukaryotic type I KH domain. The core KH domain is accompanied by additional alpha-helix and beta-sheet motifs at the C terminus. This entry includes proteins involved in pre-mRNA splicing such as KH domain-containing BBP from f ...	This entry represents eukaryotic type I KH domain. The core KH domain is accompanied by additional alpha-helix and beta-sheet motifs at the C terminus. This entry includes proteins involved in pre-mRNA splicing such as KH domain-containing BBP from fungi, KH homology domain-containing protein 4 (KHDC4, also known as BLOM7) and splicing factor 1 (SF1) from animals, and homologues from plants, including RIK. KHDC4 interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. It binds preferentially RNA with A/C rich sequences and poly-C stretches. Branchpoint binding proteins (BBP) from fungi and its mammalian homologue SF1 are required for pre-spliceosome formation [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	RNA (5'-R(PUPAPCPUPAPAPCPA)-3')	-	-	-
A, C, E, G	Branchpoint-bridging protein	RNA binding binding nucleic acid binding mRNA binding pre-mRNA binding pre-mRNA branch point binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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 mRNA cis splicing, via spliceosome	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle U2-type spliceosomal complex protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex commitment complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, C, E, G	IPR032570	Splicing factor 1, helix-hairpin domain	Domain
A, C, E, G	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
A, C, E, G	IPR004087	K Homology domain	Domain
A, C, E, G	IPR047086	Splicing factor 1, helix-hairpin domain superfamily	Homologous Superfamily
A, C, E, G	IPR001878	Zinc finger, CCHC-type	Domain
A, C, E, G	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A, C, E, G	IPR045071	KH domain-containing BBP-like	Family
A, C, E, G	IPR055256	KHDC4/BBP-like, KH-domain type I	Domain

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.