3SIV | pdb_00003siv

Structure of a hPrp31-15.5K-U4atac 5' stem loop complex, dimeric form

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nop domain	8033305	3001551	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Nop domain	8033305	3001551	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Nop domain	8033305	3001551	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Nop domain	8033305	3001551	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	L30e-like	8043738	3001739	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	L30e-like	8043738	3001739	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L30e-like	8043738	3001739	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L30e-like	8043738	3001739	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)
B	Nop_C	e3sivB1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
B	Nop_N	e3sivB2	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
K	Nop_C	e3sivK1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
K	Nop_N	e3sivK2	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
H	Nop_C	e3sivH2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
H	Nop_N	e3sivH1	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
E	Nop_C	e3sivE2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: Nop C-terminal domain	F: Nop_C	ECOD (1.6)
E	Nop_N	e3sivE1	A: alpha complex topology	X: Nop N-terminal domain (From Topology)	H: Nop N-terminal domain (From Topology)	T: Nop N-terminal domain	F: Nop_N	ECOD (1.6)
J	Ribosomal_L7Ae_1	e3sivJ1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
G	Ribosomal_L7Ae_1	e3sivG1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
D	Ribosomal_L7Ae_1	e3sivD1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
A	Ribosomal_L7Ae_1	e3sivA1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
K	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
K	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
H	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
H	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
E	1.10.287.4070	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
E	1.10.246.90	Mainly Alpha	Orthogonal Bundle	Serum Albumin	Chain A, Domain 1	CATH (4.3.0)
J	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
G	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E, H, K	PF01798	snoRNA binding domain, fibrillarin (Nop)	snoRNA binding domain, fibrillarin	-	Family
A, D, G, J	PF01248	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	U4atac snRNA	-	-	-
B, E, H, K	U4/U6 small nuclear ribonucleoprotein Prp31	RNA binding snRNA binding U4atac snRNA binding binding nucleic acid binding U4 snRNA binding ribonucleoprotein complex binding protein-containing complex binding protein-macromolecule adaptor activity molecular adaptor activity snRNP binding identical protein binding protein binding	localization cellular localization cellular process ribonucleoprotein complex localization ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process localization cellular localization cellular process ribonucleoprotein complex localization ribonucleoprotein complex biogenesis RNA metabolic process mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis RNA processing RNA splicing protein-containing complex organization spliceosomal snRNP assembly 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 metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process	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 U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex 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 U4 snRNP cellular anatomical structure small nuclear ribonucleoprotein complex organelle ribonucleoprotein complex spliceosomal complex precatalytic spliceosome membrane-enclosed lumen intracellular membraneless organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex U2-type spliceosomal complex Cajal body U2-type precatalytic spliceosome U4atac snRNP histone methyltransferase complex catalytic complex MLL1/2 complex transferase complex MLL1 complex methyltransferase complex
A, D, G, J	NHP2-like protein 1	RNA binding snRNA binding U4atac snRNA binding binding nucleic acid binding U3 snoRNA binding snoRNA binding U4 snRNA binding box C/D sno(s)RNA binding ATPase binding protein binding enzyme binding	sexual reproduction reproductive process fertilization single fertilization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process cellular component biogenesis sexual reproduction reproductive process fertilization single fertilization ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process ribosomal small subunit biogenesis nucleic acid metabolic process cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process maturation of SSU-rRNA cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process RNA processing rRNA metabolic process protein-containing complex organization small nucleolar ribonucleoprotein complex assembly protein-RNA complex assembly cellular component organization protein-RNA complex organization cellular component assembly protein-containing complex assembly box C/D snoRNP assembly RNA splicing mRNA processing mRNA metabolic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex nuclear protein-containing complex spliceosomal complex ribonucleoprotein complex precatalytic spliceosome spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex nucleoplasm box C/D methylation guide snoRNP complex sno(s)RNA-containing ribonucleoprotein complex box C/D RNP complex preribosome small-subunit processome dense fibrillar component U2-type spliceosomal complex U2-type precatalytic spliceosome U4atac snRNP

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E, H, K	IPR042239	Nop, C-terminal domain	Homologous Superfamily
B, E, H, K	IPR019175	Prp31 C-terminal	Domain
B, E, H, K	IPR002687	Nop domain	Domain
B, E, H, K	IPR012976	NOSIC	Domain
B, E, H, K	IPR027105	U4/U6 small nuclear ribonucleoprotein Prp31	Family
B, E, H, K	IPR036070	Nop domain superfamily	Homologous Superfamily
A, D, G, J	IPR002415	H/ACA ribonucleoprotein complex, subunit Nhp2-like	Family
A, D, G, J	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
A, D, G, J	IPR018492	Ribosomal protein eL8/Nhp2 family	Family
A, D, G, J	IPR050257	Large ribosomal subunit protein eL8/uL1-like	Family
A, D, G, J	IPR004038	Ribosomal protein eL8/eL30/eS12/Gadd45	Domain
A, D, G, J	IPR004037	Large ribosomal subunit protein eL8-like, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E, H, K	Pharos: Q8WWY3	retinitis pigmentosa retinitis pigmentosa 11 alcoholic liver cirrhosis malignant ependymoma ovarian cancer cone-rod dystrophy medulloblastoma psoriasis Gaucher disease night blindness retinal degeneration Takayasu arteritis
A, D, G, J	Pharos: P55769	glioblastoma ovarian cancer lung cancer psoriasis osteosarcoma Sjogren syndrome

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.