4JKB

Open and closed forms of V1788D human PRP8 RNase H-like domain with bound Mg ion

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4jkba_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Prp8 beta-finger domain-like	Pre-mRNA splicing factor 8, Prp8 / Spp42	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4jkbb_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Prp8 beta-finger domain-like	Pre-mRNA splicing factor 8, Prp8 / Spp42	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8041105	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8041105	3000143	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)
A	PRP8_domainIV	e4jkbA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PRP8_domainIV	ECOD (1.6)
B	PRP8_domainIV	e4jkbB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PRP8_domainIV	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.230	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.20.80.40	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein	Prp8 RNase H domain, fingers region	CATH (4.3.0)
B	3.30.420.230	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	1.20.80.40	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein	Prp8 RNase H domain, fingers region	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12134	PRP8 domain IV core (PRP8_domainIV)	PRP8 domain IV core	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The dom ...	This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with Pfam:PF10597, Pfam:PF10596, Pfam:PF10598, Pfam:PF08083, Pfam:PF08082, Pfam:PF01398, Pfam:PF08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pre-mRNA-processing-splicing factor 8	RNA binding snRNA binding binding organic cyclic compound binding nucleic acid binding U1 snRNA binding U6 snRNA binding polyubiquitin modification-dependent protein binding protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding U5 snRNA binding U2 snRNA binding pre-mRNA binding RNA binding snRNA binding binding organic cyclic compound binding nucleic acid binding U1 snRNA binding U6 snRNA binding polyubiquitin modification-dependent protein binding protein binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding U5 snRNA binding U2 snRNA binding pre-mRNA binding pre-mRNA intronic binding	RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process RNA splicing, via transesterification reactions biosynthetic process organic substance biosynthetic process RNA splicing cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process RNA splicing, via transesterification reactions biosynthetic process organic substance biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process ribonucleoprotein complex biogenesis mRNA processing spliceosomal tri-snRNP complex assembly protein-RNA complex assembly cellular component organization cellular component biogenesis protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis protein-containing complex organization spliceosomal snRNP assembly mRNA metabolic process mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to stimulus response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin response to cytokine cellular response to tumor necrosis factor cellular response to cytokine stimulus response to tumor necrosis factor	membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen U2-type spliceosomal complex protein-containing complex catalytic complex nuclear protein-containing complex U2-type catalytic step 1 spliceosome spliceosomal complex ribonucleoprotein complex catalytic step 1 spliceosome catalytic step 2 spliceosome spliceosomal snRNP complex Sm-like protein family complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex small nuclear ribonucleoprotein complex U2-type precatalytic spliceosome precatalytic spliceosome U5 snRNP U2-type catalytic step 2 spliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012984	PROCT domain	Domain
A, B	IPR012591	PRO8NT domain	Domain
A, B	IPR019580	Pre-mRNA-processing-splicing factor 8, U6-snRNA-binding	Domain
A, B	IPR027652	Pre-mRNA-processing-splicing factor 8	Family
A, B	IPR043172	Prp8 RNase domain IV, palm region	Homologous Superfamily
A, B	IPR012592	PROCN domain	Domain
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR043173	Prp8 RNase domain IV, fingers region	Homologous Superfamily
A, B	IPR021983	PRP8 domain IV core	Domain
A, B	IPR019581	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding	Domain
A, B	IPR037518	MPN domain	Domain
A, B	IPR019582	RNA recognition motif, spliceosomal PrP8	Domain
A, B	IPR042516	Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain superfamily	Homologous Superfamily
A, B	IPR000555	JAB1/MPN/MOV34 metalloenzyme domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q6P2Q9	retinitis pigmentosa retinitis pigmentosa 13 HIV infectious disease Acute Cerebrovascular Accidents brain aneurysm cone-rod dystrophy malignant ependymoma pancreatic ductal adenocarcinoma acute myeloid leukemia diabetes mellitus oligodendroglioma retinal degeneration astrocytic tumor cerebrovascular disorder glioblastoma retinitis pigmentosa retinitis pigmentosa 13 HIV infectious disease Acute Cerebrovascular Accidents brain aneurysm cone-rod dystrophy malignant ependymoma pancreatic ductal adenocarcinoma acute myeloid leukemia diabetes mellitus oligodendroglioma retinal degeneration astrocytic tumor cerebrovascular disorder glioblastoma Hodgkins lymphoma ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.