4BWS | pdb_00004bws

Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD.

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)
F	d4bwsf1	Alpha and beta proteins (a+b)	GYF/BRK domain-like	GYF domain	GYF domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4bwsf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4bwsc1	Alpha and beta proteins (a+b)	GYF/BRK domain-like	GYF domain	GYF domain	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4bwsc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4bwsd_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	spliceosomal protein U5-15Kd	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4bwsa_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	spliceosomal protein U5-15Kd	automated matches	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)
F	SCOP2B Superfamily	GYF domain-like	8032414	3001702	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GYF domain-like	8032414	3001702	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8044390	3000031	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin-like	8044390	3000031	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)
F	GYF	e4bwsF1	A: a+b two layers	X: GYF/BRK domain-like	H: GYF domain (From Topology)	T: GYF domain	F: GYF	ECOD (1.6)
C	GYF	e4bwsC1	A: a+b two layers	X: GYF/BRK domain-like	H: GYF domain (From Topology)	T: GYF domain	F: GYF	ECOD (1.6)
D	DIM1	e4bwsD1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: DIM1	ECOD (1.6)
A	DIM1	e4bwsA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: DIM1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.30.1490.40	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF02213	GYF domain (GYF)	GYF domain	The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein Swiss:O95400.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2	ribonucleoprotein complex binding protein-containing complex binding binding	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 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 cellular process metabolic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle organelle lumen fibrillar center organelle membraneless organelle nuclear lumen U5 snRNP spliceosomal snRNP complex protein-containing complex nuclear protein-containing complex Sm-like protein family complex small nuclear ribonucleoprotein complex ribonucleoprotein complex nuclear speck ribonucleoprotein granule nuclear body nucleoplasm supramolecular complex nuclear ribonucleoprotein granule
B, E	POLYGLUTAMINE-BINDING PROTEIN 1	transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity ribonucleoprotein complex binding protein-containing complex binding binding DNA binding nucleic acid binding double-stranded DNA binding	regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms response to stimulus regulation of response to external stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of immune response regulation of response to stress response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process regulation of biological process positive regulation of innate immune response defense response immune response response to other organism regulation of innate immune response biological regulation defense response to symbiont response to external stimulus regulation of response to stimulus immune system process defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cellular response to nitrogen compound cellular response to stimulus cellular response to dsRNA cellular response to exogenous dsRNA response to dsRNA response to nitrogen compound response to exogenous dsRNA cellular response to chemical stimulus response to chemical cellular process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process regulation of defense response to virus defense response to virus positive regulation of defense response to virus by host regulation of defense response to virus by host response to virus regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation dendrite development neuron projection morphogenesis regulation of dendrite morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis regulation of anatomical structure morphogenesis system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process positive regulation of cellular process positive regulation of type I interferon production type I interferon production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production regulation of type I interferon production RNA processing RNA splicing regulation of RNA splicing alternative mRNA splicing, via spliceosome 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 cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle membraneless organelle cytoplasm supramolecular complex membrane-bounded organelle cell projection cellular anatomical structure organelle cilium plasma membrane bounded cell projection intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear ribonucleoprotein granule nuclear lumen cytosol cytoskeleton microtubule cytoskeleton neuron projection cytoplasm neuron projection cytoplasmic region plasma membrane bounded cell projection cytoplasm neuronal ribonucleoprotein granule ciliary basal body microtubule organizing center
A, D	THIOREDOXIN-LIKE PROTEIN 4A	-	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 cell division	membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle U2-type precatalytic spliceosome intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome membrane-bounded organelle U2-type spliceosomal complex protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle U2-type precatalytic spliceosome intracellular organelle cellular anatomical structure spliceosomal complex organelle ribonucleoprotein complex precatalytic spliceosome cytoplasm cytosol U5 snRNP spliceosomal snRNP complex Sm-like protein family complex small nuclear ribonucleoprotein complex U4/U6 x U5 tri-snRNP complex spliceosomal tri-snRNP complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR003169	GYF domain	Domain
C, F	IPR035445	GYF-like domain superfamily	Homologous Superfamily
C, F	IPR039905	CD2 antigen cytoplasmic tail-binding protein 2/Lin1	Family
B, E	IPR036020	WW domain superfamily	Homologous Superfamily
B, E	IPR001202	WW domain	Domain
A, D	IPR004123	Dim1 family	Family
A, D	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: O95400	diabetes mellitus osteosarcoma ovarian cancer
B, E	Pharos: O60828	Renpenning syndrome atrial septal defect microcephaly hereditary spastic paraplegia autism, susceptibility to, X-linked 2 intellectual disability plasma cell myeloma Spastic Paraplegia, Hereditary coloboma malignant glioma microlissencephaly ovarian cancer X-linked intellectual disability, Golabi-Ito-hall type colorectal cancer hamel cerebro-palato-cardiac syndrome Renpenning syndrome atrial septal defect microcephaly hereditary spastic paraplegia autism, susceptibility to, X-linked 2 intellectual disability plasma cell myeloma Spastic Paraplegia, Hereditary coloboma malignant glioma microlissencephaly ovarian cancer X-linked intellectual disability, Golabi-Ito-hall type colorectal cancer hamel cerebro-palato-cardiac syndrome osteosarcoma psoriasis Sjogren syndrome X-linked syndromic intellectual disability genetic endocrine growth disease
A, D	Pharos: P83876	Burn-Mckeown syndrome choanal atresia-hearing loss-cardiac defects-craniofacial dysmorphism syndrome astrocytic tumor choanal atresia glioblastoma malignant ependymoma ovarian cancer atypical teratoid rhabdoid tumor intellectual disability malignant glioma plasma cell myeloma diabetes mellitus lung cancer osteosarcoma psoriasis

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.