Annotations: 7M22

Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth N]	SCOP2B Superfamily	galactose-binding domain-like	8069035	3000087	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)
D [auth N]	F-actin_cap_A	e7m22N1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: F-actin_cap_A	ECOD (v295.2)
C [auth E]	Utp12	e7m22E1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Utp12	ECOD (v295.2)
B [auth D]	Utp12	e7m22D1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Utp12	ECOD (v295.2)
A [auth C]		e7m22C1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F:	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth N]	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain
D [auth N]	PF00431	CUB domain (CUB)	CUB domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth N]	Neuropilin-2	molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity protein binding binding growth factor binding cytokine binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity protein binding binding growth factor binding cytokine binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups vascular endothelial growth factor receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity catalytic activity cation binding ion binding metal ion binding small molecule binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	developmental process multicellular organismal process cranial nerve morphogenesis parasympathetic nervous system development nervous system development anatomical structure morphogenesis multicellular organism development cranial nerve structural organization nerve development cranial nerve development central nervous system development preganglionic parasympathetic fiber development anatomical structure development anatomical structure arrangement developmental process multicellular organismal process cranial nerve morphogenesis parasympathetic nervous system development nervous system development anatomical structure morphogenesis multicellular organism development cranial nerve structural organization nerve development cranial nerve development central nervous system development preganglionic parasympathetic fiber development anatomical structure development anatomical structure arrangement facial nerve morphogenesis autonomic nervous system development animal gross anatomical part developmental process facial nerve structural organization system development facial nerve development cranial ganglion development tissue development ganglion development facioacoustic ganglion development positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cellular process cell motility locomotion positive regulation of cellular process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development cellular developmental process neural crest cell development cell development mesenchyme development mesenchymal cell migration cell differentiation ameboidal-type cell migration neural crest cell migration stem cell development neural crest cell differentiation animal organ development stem cell differentiation neural crest cell migration involved in autonomic nervous system development mesenchymal cell differentiation axon extension axonogenesis developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell growth cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis axon extension involved in axon guidance cellular component organization or biogenesis neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth axon guidance axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis generation of neurons neuron projection guidance neuron development sympathetic neuron projection guidance blastoderm segmentation segmentation pattern specification process embryo development ventral trunk neural crest cell migration embryonic pattern specification regionalization trunk neural crest cell migration trunk segmentation sympathetic nervous system development sympathetic ganglion development sympathetic neuron projection extension motor neuron axon guidance branchiomotor neuron axon guidance heart development cardiac chamber morphogenesis heart morphogenesis cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis animal organ morphogenesis gonadotrophin-releasing hormone neuronal migration to the hypothalamus hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development neuron migration forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration trigeminal nerve development trigeminal nerve structural organization trigeminal nerve morphogenesis cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction cell adhesion ganglion morphogenesis dorsal root ganglion morphogenesis tissue morphogenesis dorsal root ganglion development cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation sensory neuron axon guidance regulation of cellular component organization postsynapse organization regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality trigeminal ganglion development vestibulocochlear nerve structural organization vestibulocochlear nerve development vestibulocochlear nerve morphogenesis	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex semaphorin receptor complex signaling receptor complex glutamatergic synapse cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex semaphorin receptor complex signaling receptor complex glutamatergic synapse extracellular region axon cell projection neuron projection plasma membrane bounded cell projection
C [auth E]	UL131A	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane
B [auth D]	Envelope glycoprotein UL130	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component virion membrane
A [auth C]	Envelope protein UL128	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth N]	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
D [auth N]	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
D [auth N]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
D [auth N]	IPR000998	MAM domain	Domain
D [auth N]	IPR000859	CUB domain	Domain
D [auth N]	IPR022579	Neuropilin, C-terminal	Domain
D [auth N]	IPR000421	Coagulation factor 5/8, C-terminal domain	Domain
D [auth N]	IPR014648	Neuropilin	Family
D [auth N]	IPR050633	Neuropilin/Multicopper Oxidase/Coagulation Factor	Family
B [auth D]	IPR021038	Herpesvirus UL130, cytomegalovirus	Family
A [auth C]	IPR057762	UL128-like, Cytomegalovirus	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth N]	: O60462	visual epilepsy interstitial cystitis tuberculosis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Absence Seizures astrocytic tumor autism ovarian cancer primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma visual epilepsy interstitial cystitis tuberculosis large cell medulloblastoma malignant colon neoplasm malignant mesothelioma Absence Seizures astrocytic tumor autism ovarian cancer primitive neuroectodermal tumor cystic fibrosis gastric carcinoma glioblastoma invasive ductal breast carcinoma lung cancer malignant ependymoma malignant pancreatic neoplasm adenoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm lung carcinoma malignant glioma MALT lymphoma adrenal cortex carcinoma atypical teratoid rhabdoid tumor osteosarcoma breast cancer pilocytic astrocytoma subependymal giant cell astrocytoma

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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.