3D12 | pdb_00003d12

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3

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)
B	d3d12b_	All beta proteins	Cupredoxin-like	Cupredoxins	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth E]	d3d12e_	All beta proteins	Cupredoxin-like	Cupredoxins	automated matches	automated matches	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	Sialidases	8086578	3001607	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Sialidases	8086578	3001607	SCOP2B (2022-06-29)
B	SCOP2 Family	Ephrin ectodomain	8061912	4002092	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cupredoxins	8061913	3000886	SCOP2 (2022-06-29)
D [auth E]	SCOP2B Superfamily	Cupredoxins	8061913	3000886	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		e3d12A1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
C [auth D]		e3d12D1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)
B		e3d12B1	A: Profilin-like	X: sensor domains	H: sensor domains	T: Methyltransf_2	F:	ECOD (20:10:01)
D [auth E]		e3d12E1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Transmembrane protein 14A	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
C [auth D]	2.120.10.10	Mainly Beta	6 Propeller	Neuraminidase		CATH (4.3.0)
B	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)
D [auth E]	2.60.40.420	Mainly Beta	Sandwich	Immunoglobulin-like	Cupredoxins - blue copper proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E]	PF00812	Ephrin (Ephrin)	Ephrin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D]	Hemagglutinin-neuraminidase	identical protein binding protein binding binding hydrolase activity, acting on glycosyl bonds alpha-sialidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity exo-alpha-sialidase activity catalytic activity host cell surface binding host cell surface receptor binding	import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell membrane fusion involved in viral entry into host cell virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell adhesion of symbiont to host	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane
B, D [auth E]	Ephrin-B3	protein binding binding signaling receptor binding ephrin receptor binding	multicellular organismal process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of biological process cellular component organization regulation of presynapse assembly cellular component biogenesis multicellular organism development cellular component assembly regulation of presynapse organization cell junction assembly anatomical structure development regulation of synapse structure or activity multicellular organismal process positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization positive regulation of biological process cellular component organization regulation of presynapse assembly cellular component biogenesis multicellular organism development cellular component assembly regulation of presynapse organization cell junction assembly anatomical structure development regulation of synapse structure or activity cellular component organization or biogenesis regulation of synapse assembly synapse organization regulation of biological quality positive regulation of cellular process system development developmental process regulation of biological process positive regulation of presynapse assembly biological regulation presynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization cellular process synapse assembly presynapse assembly trans-synaptic signaling regulation of signaling trans-synaptic signaling by trans-synaptic complex signaling trans-synaptic signaling, modulating synaptic transmission modulation of chemical synaptic transmission trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission cell-cell signaling cell communication chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular response to stimulus cell surface receptor signaling pathway response to stimulus cell surface receptor protein tyrosine kinase signaling pathway signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway neuron recognition axon choice point recognition cell recognition negative regulation of biological process regulation of cell differentiation regulation of neurogenesis regulation of cell development negative regulation of cellular component organization regulation of cell projection organization negative regulation of axonogenesis negative regulation of multicellular organismal process regulation of neuron projection development regulation of developmental process regulation of nervous system development negative regulation of neurogenesis regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of developmental process negative regulation of neuron projection development negative regulation of cell development regulation of plasma membrane bounded cell projection organization regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation immune system process lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation adult walking behavior adult locomotory behavior behavior adult behavior locomotory behavior walking behavior positive regulation of cell communication positive regulation of synaptic transmission positive regulation of signaling	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region hippocampal mossy fiber to CA3 synapse presynapse presynaptic membrane glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D]	IPR016285	Haemagglutinin-neuraminidase	Family
A, C [auth D]	IPR036278	Sialidase superfamily	Homologous Superfamily
A, C [auth D]	IPR000665	Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus	Family
B, D [auth E]	IPR019765	Ephrin, conserved site	Conserved Site
B, D [auth E]	IPR008972	Cupredoxin	Homologous Superfamily
B, D [auth E]	IPR031328	Ephrin	Family
B, D [auth E]	IPR001799	Ephrin receptor-binding domain	Domain

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.