7T4S

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF17488	e7t4sA2	A: beta sandwiches	X: C-terminal domain of envelope glycoprotein H (From Topology)	H: C-terminal domain of envelope glycoprotein H (From Topology)	T: C-terminal domain of envelope glycoprotein H	F: PF17488	ECOD (1.6)
A	PF02489	e7t4sA1	A: a+b complex topology	X: gH main domain (From Topology)	H: gH main domain (From Topology)	T: gH main domain	F: PF02489	ECOD (1.6)
J [auth I]	PF07686	e7t4sI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B	PF01801	e7t4sB1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF01801	ECOD (1.6)
B	PF01801	e7t4sB2	A: alpha arrays	X: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain (From Topology)	H: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain (From Topology)	T: beta-herpesvirus envelope glycoprotein L (gL) N-terminal domain	F: PF01801	ECOD (1.6)
C	F_UNCLASSIFIED	e7t4sC2	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e7t4sC1	A: beta barrels	X: UL128 C-terminal domain (From Topology)	H: UL128 C-terminal domain (From Topology)	T: UL128 C-terminal domain	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF11668	e7t4sD1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF11668	ECOD (1.6)
D	PF11668	e7t4sD2	A: beta barrels	X: UL131A-like	H: UL130 C-terminal domain (From Topology)	T: UL130 C-terminal domain	F: PF11668	ECOD (1.6)
E	F_UNCLASSIFIED	e7t4sE1	A: beta barrels	X: UL131A-like	H: UL131A (From Topology)	T: UL131A	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF00431	e7t4sF2	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain (From Topology)	T: Spermadhesin, CUB domain	F: PF00431	ECOD (1.6)
F	PF00754	e7t4sF1	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)
G [auth H]	PF07686	e7t4sH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth J]	PF07686	e7t4sJ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth K]	PF07686	e7t4sK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
J [auth I]	Light Chain	IGKV3	Kappa	envelope glycoprotein ul130 \| envelope glycoprotein l	SAbDab (2024-05-03)
G [auth H]	Heavy Chain	IGHV3	-	envelope glycoprotein ul130 \| envelope glycoprotein l	SAbDab (2024-05-03)
H [auth J]	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2024-05-03)
I [auth K]	Light Chain	IGKV1	Kappa	envelope glycoprotein h	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17488	Herpesvirus glycoprotein H C-terminal domain (Herpes_glycoH_C)	Herpesvirus glycoprotein H C-terminal domain	Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein [2]. Complex formation between gH and gL has been demonstrated in both virions and infected cells [1]. This entry represents the C-terminal domain.	Domain
A	PF02489	Herpesvirus glycoprotein H main domain (Herpes_glycop_H)	Herpesvirus glycoprotein H main domain	Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein [2]. Complex formation between gH and gL has been demonstrated in both virions and infected cells [1].	Domain
B	PF01801	Cytomegalovirus glycoprotein L (Cytomega_gL)	Cytomegalovirus glycoprotein L	-	Family
D	PF11668	HCMV glycoprotein pUL130 (Gp_UL130)	HCMV glycoprotein pUL130	-	Family
F	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
F	PF00431	CUB domain (CUB)	CUB domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Envelope glycoprotein H	-	membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction 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	cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular membrane-bounded organelle host intracellular part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell endosome host intracellular region
J [auth I]	Fab 8I21 light chain	-	-	-
B	Envelope glycoprotein L	-	membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction 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	cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell cytoplasm cell periphery plasma membrane membrane cellular anatomical entity virion component viral membrane viral envelope host cell plasma membrane host cellular component host cell part host cell membrane virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region host cell cytoplasm part
C	Envelope protein UL128	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction 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 membrane cellular anatomical entity virion membrane
D	Envelope glycoprotein UL130	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction 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 membrane cellular anatomical entity virion membrane
E	Envelope protein UL131A	-	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction 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 membrane cellular anatomical entity virion membrane
F	Neuropilin-2	cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity growth factor binding cytokine binding catalytic activity, acting on a protein cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity semaphorin receptor activity 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 heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development cellular developmental process cell projection organization developmental process multicellular organismal process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis sympathetic neuron projection guidance neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cellular process blastoderm segmentation segmentation neural crest cell development pattern specification process mesenchyme development embryo development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation ventral trunk neural crest cell migration embryonic pattern specification animal organ development regionalization trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation axonogenesis motor neuron axon guidance branchiomotor neuron axon guidance axon guidance axon development cell morphogenesis involved in neuron differentiation heart development cardiac chamber morphogenesis heart morphogenesis circulatory system development 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 central nervous system development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration chemotaxis negative chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion cell adhesion sensory neuron axon guidance regulation of biological process regulation of cellular component organization regulation of cellular process postsynapse organization biological regulation regulation of postsynapse organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality cranial nerve morphogenesis vestibulocochlear nerve structural organization cranial nerve structural organization vestibulocochlear nerve development vestibulocochlear nerve morphogenesis anatomical structure arrangement parasympathetic nervous system development preganglionic parasympathetic fiber development facial nerve morphogenesis autonomic nervous system development facial nerve structural organization facial nerve development positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of biological process positive regulation of cell migration positive regulation of epithelial cell migration tissue migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration positive regulation of cellular process epithelium migration regulation of locomotion positive regulation of endothelial cell migration blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development neural crest cell migration involved in autonomic nervous system development axon extension developmental growth cell growth axon extension involved in axon guidance neuron projection extension involved in neuron projection guidance neuron projection extension developmental cell growth growth developmental growth involved in morphogenesis sympathetic nervous system development sympathetic ganglion development sympathetic neuron projection extension trigeminal nerve development trigeminal nerve structural organization trigeminal nerve morphogenesis cellular response to stimulus cell surface receptor signaling pathway semaphorin-plexin signaling pathway signaling cell communication signal transduction 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 trigeminal ganglion development response to organic substance response to cytokine response to leukemia inhibitory factor cellular response to leukemia inhibitory factor cellular response to chemical stimulus cellular response to cytokine stimulus cellular response to organic substance	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse axon cell projection neuron projection plasma membrane bounded cell projection extracellular region
G [auth H]	Fab 8I21 heavy chain	-	-	-
H [auth J]	Fab 13H11 heavy chain	-	-	-
I [auth K]	Fab 13H11 light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038172	Herpesvirus glycoprotein H, C-terminal domain superfamily	Homologous Superfamily
A	IPR003493	Herpesvirus glycoprotein H	Family
A	IPR035305	Herpesvirus glycoprotein H, C-terminal	Domain
B	IPR002689	Cytomegalovirus glycoprotein L	Family
D	IPR021038	Herpesvirus UL130, cytomegalovirus	Family
F	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
F	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
F	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
F	IPR014648	Neuropilin	Family
F	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
F	IPR000998	MAM domain	Domain
F	IPR000859	CUB domain	Domain
F	IPR022579	Neuropilin, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F	Pharos: O60462	visual epilepsy tuberculosis interstitial cystitis 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 tuberculosis interstitial cystitis 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 pilocytic astrocytoma breast cancer subependymal giant cell astrocytoma

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 R01GM133198.