4OUL | pdb_00004oul

Crystal structure of human Caprin-2 C1q domain

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	d4oula1	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4oula2	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4oulb_	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4oulc_	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4ould_	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4oule_	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d4oulf_	All beta proteins	TNF-like	TNF-like	automated matches	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)
A	SCOP2B Superfamily	TNF-like	8070848	3000061	SCOP2B (2022-06-29)
B	SCOP2 Family	TNF-like	8070847	4000294	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TNF-like	8070848	3000061	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	TNF-like	8070848	3000061	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TNF-like	8070848	3000061	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TNF-like	8070848	3000061	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TNF-like	8070848	3000061	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	C1q	e4oulA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)
B	C1q	e4oulB1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)
C	C1q	e4oulC1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)
D	C1q	e4oulD1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)
E	C1q	e4oulE1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)
F	C1q	e4oulF1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: C1q	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00386	C1q domain (C1q)	C1q domain	C1q is a subunit of the C1 enzyme complex that activates the serum complement system.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Caprin-2	protein binding binding signaling receptor binding RNA binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process dorsal/ventral pattern formation dorsal/ventral axis specification anatomical structure development pattern specification process axis specification regionalization cellular developmental process cell differentiation cellular process regulation of cellular process negative regulation of biological process developmental process multicellular organism development multicellular organismal process dorsal/ventral pattern formation dorsal/ventral axis specification anatomical structure development pattern specification process axis specification regionalization cellular developmental process cell differentiation cellular process regulation of cellular process negative regulation of biological process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process positive regulation of canonical Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of nervous system development cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell morphogenesis regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of dendrite morphogenesis positive regulation of cell projection organization system development regulation of cell projection organization positive regulation of cell development nervous system development positive regulation of cell morphogenesis generation of neurons regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell morphogenesis regulation of nervous system development neurogenesis positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization positive regulation of dendrite morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization positive regulation of dendritic spine morphogenesis positive regulation of dendritic spine development regulation of synapse structure or activity synapse organization regulation of biological quality dendritic spine morphogenesis dendritic spine development postsynapse organization dendritic spine organization regulation of postsynapse organization regulation of dendritic spine development positive regulation of neuron projection development regulation of synapse organization cell junction organization regulation of dendritic spine morphogenesis neuron projection organization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex receptor complex centrosome microtubule organizing center cytoskeleton membraneless organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex receptor complex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cytosol cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR041637	Caprin-1 dimerization domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR028816	Caprin	Family
A, B, C, D, E A, B, C, D, E, F	IPR022070	Cytoplasmic activation/proliferation-associated protein-1 C term	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001073	C1q domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q6IMN6	Alzheimer disease large cell medulloblastoma myopathy pancreatic ductal adenocarcinoma progressive supranuclear palsy amyotrophic lateral sclerosis lung cancer osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer malignant mesothelioma ovarian cancer Pick disease

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.