5YBZ | pdb_00005ybz

High resolution structure of complement C1q-like protein 3 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ybza1	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5ybza3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5ybza2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d5ybzc1	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d5ybzc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth C]	d5ybzc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth D]	d5ybzd1	All beta proteins	TNF-like	TNF-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth D]	d5ybzd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth D]	d5ybzd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	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	8070840	3000061	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	TNF-like	8070840	3000061	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	TNF-like	8070840	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	IMS_HHH_1	e5ybzA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: IMS_HHH_1	ECOD (v294.1)
B [auth C]	Chlorophyllase2	e5ybzC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)
C [auth D]	Chlorophyllase2	e5ybzD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (v294.1)

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 [auth C]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C [auth D]	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 [auth C], C [auth D]	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 [auth C], C [auth D]	Complement C1q-like protein 3	identical protein binding protein binding binding	protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle protein localization to postsynaptic specialization membrane protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse biological regulation localization within membrane protein localization to membrane protein-containing complex localization neurotransmitter receptor localization to postsynaptic specialization membrane localization regulation of postsynaptic membrane neurotransmitter receptor levels macromolecule localization protein localization to organelle cellular process protein localization to postsynapse intracellular protein localization regulation of biological quality protein localization to cell junction receptor localization to synapse regulation of biological process regulation of cellular component organization regulation of cellular process cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization cellular component organization or biogenesis multicellular organismal process cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly postsynaptic density organization anatomical structure development system development developmental process postsynapse organization organelle assembly postsynaptic specialization assembly postsynapse assembly nervous system development excitatory synapse assembly organelle organization postsynaptic specialization organization synapse assembly postsynaptic density assembly	protein-containing complex collagen trimer cellular anatomical structure neuron to neuron synapse synapse cell junction hippocampal mossy fiber to CA3 synapse extracellular region synaptic cleft glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth D]	IPR008160	Collagen triple helix repeat	Repeat
A, B [auth C], C [auth D]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B [auth C], C [auth D]	IPR001073	C1q domain	Domain
A, B [auth C], C [auth D]	IPR050822	Cerebellin Synaptic Organizer	Family

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.