7LBF

CryoEM structure of the HCMV Trimer gHgLgO in complex with human Platelet-derived growth factor receptor alpha and neutralizing fabs 13H11 and MSL-109

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
E	d7lbfe_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d7lbfg_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF17488	e7lbfA2	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	e7lbfA1	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)
B	PF01801	e7lbfB1	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	e7lbfB2	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)
D	PF00047	e7lbfD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF00047	ECOD (1.6)
D	PF07679	e7lbfD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07679	ECOD (1.6)
D	PF21339	e7lbfD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF21339	ECOD (1.6)
E	PF07686	e7lbfE1	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)
F	PF07686	e7lbfF1	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)
G	PF07686	e7lbfG1	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	PF07686	e7lbfH1	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
E	Light Chain	IGKV1	Kappa	envelope glycoprotein h	SAbDab (2024-04-26)
F	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2024-04-26)
G	Light Chain	IGKV2	Kappa	envelope glycoprotein h	SAbDab (2024-04-26)
H	Heavy Chain	IGHV3	-	envelope glycoprotein h	SAbDab (2024-04-26)

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
C	PF07982	Herpes UL74 glycoproteins (Herpes_UL74)	Herpes UL74 glycoproteins	-	Family
D	PF07679	Immunoglobulin I-set domain (I-set)	Immunoglobulin I-set 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
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 glycoprotein O	-	-	virion component viral membrane viral envelope
D	Isoform 3 of Platelet-derived growth factor receptor alpha	protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding platelet-derived growth factor binding growth factor binding platelet-derived growth factor receptor activity platelet-derived growth factor alpha-receptor activity identical protein binding protein homodimerization activity protein dimerization activity vascular endothelial growth factor binding vascular endothelial growth factor receptor activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process positive regulation of signaling multicellular organismal process cell activation cell surface receptor signaling pathway platelet-derived growth factor receptor-alpha signaling pathway platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway chemotaxis positive regulation of locomotion regulation of response to external stimulus response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to external stimulus taxis response to chemical regulation of locomotion locomotion cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization cellular response to growth factor stimulus positive regulation of cell population proliferation positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway cellular response to endogenous stimulus VEGF-activated platelet-derived growth factor receptor signaling pathway cell population proliferation response to endogenous stimulus vascular endothelial growth factor signaling pathway regulation of cell population proliferation cellular response to vascular endothelial growth factor stimulus response to growth factor regulation of body fluid levels wound healing homotypic cell-cell adhesion hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation regulation of biological quality response to wounding platelet activation genitalia development developmental process reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male sex differentiation multicellular organism development anatomical structure development male genitalia development reproductive structure development system development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development anatomical structure morphogenesis embryo development ending in birth or egg hatching skeletal system development animal organ morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis metanephric glomerulus vasculature development glomerulus vasculature morphogenesis metanephric glomerulus development angiogenesis renal system development kidney vasculature development renal system vasculature development tube morphogenesis glomerular capillary formation metanephros development nephron development metanephric nephron development blood vessel development blood vessel morphogenesis tube development metanephric glomerulus morphogenesis vasculature development circulatory system development glomerulus development metanephric glomerulus vasculature morphogenesis glomerulus morphogenesis anatomical structure formation involved in morphogenesis glomerulus vasculature development kidney development kidney vasculature morphogenesis metanephric glomerular capillary formation renal system vasculature morphogenesis in utero embryonic development protein phosphorylation organonitrogen compound metabolic process protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process cell chemotaxis cellular response to chemical stimulus cell migration cell motility cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to organic substance response to amino acid cellular biosynthetic process signal transduction involved in regulation of gene expression organic substance biosynthetic process regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process fat cell differentiation cellular developmental process cell differentiation white fat cell differentiation negative regulation of biological process regulation of cell activation negative regulation of platelet activation regulation of response to wounding regulation of coagulation regulation of response to stress negative regulation of cellular process regulation of multicellular organismal process regulation of hemostasis negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of cell activation negative regulation of hemostasis regulation of platelet activation negative regulation of coagulation negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process sensory organ development retina vasculature development in camera-type eye eye development retina development in camera-type eye visual system development camera-type eye development sensory system development gonad development male gonad development development of primary male sexual characteristics development of primary sexual characteristics Leydig cell differentiation positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade head development face morphogenesis head morphogenesis face development body morphogenesis odontogenesis of dentin-containing tooth odontogenesis regulation of hormone levels steroid metabolic process hormone metabolic process estrogen metabolic process organic cyclic compound metabolic process lipid metabolic process regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization embryonic cranial skeleton morphogenesis cranial skeletal system development fibroblast proliferation regulation of fibroblast proliferation positive regulation of fibroblast proliferation respiratory tube development lung development respiratory system development regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to stress adrenal gland development endocrine system development gland development regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration regulation of phospholipase activity positive regulation of phospholipase activity regulation of catalytic activity positive regulation of catalytic activity positive regulation of phospholipase C activity positive regulation of lipase activity regulation of molecular function positive regulation of molecular function positive regulation of hydrolase activity regulation of phospholipase C activity regulation of hydrolase activity regulation of lipase activity cardiac muscle cell development cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly cell development muscle cell differentiation striated muscle tissue development cellular component biogenesis muscle structure development striated muscle cell development cellular anatomical entity morphogenesis cellular component assembly muscle cell development cardiac cell development muscle tissue development heart development actomyosin structure organization organelle assembly cardiac muscle tissue development cardiac muscle cell differentiation tissue development cardiocyte differentiation myofibril assembly cardiac myofibril assembly striated muscle cell differentiation supramolecular fiber organization digestive system development embryonic digestive tract morphogenesis digestive tract development digestive tract morphogenesis embryonic digestive tract development hemopoiesis hematopoietic progenitor cell differentiation regulation of developmental process regulation of cell differentiation stem cell differentiation mesenchymal stem cell differentiation regulation of stem cell differentiation regulation of mesenchymal stem cell differentiation roof of mouth development rhythmic process ovulation cycle process luteinization female gonad development multicellular organismal reproductive process female sex differentiation development of primary female sexual characteristics ovulation cycle	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm protein-containing complex receptor complex membrane-bounded organelle intracellular organelle Golgi apparatus cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm protein-containing complex receptor complex membrane-bounded organelle intracellular organelle Golgi apparatus organelle intracellular membrane-bounded organelle endomembrane system cell projection actin-based cell projection microvillus plasma membrane bounded cell projection cell junction cilium nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane
E	Fab 13H11 light chain	-	-	-
F	Fab 13H11 heavy chain	-	-	-
G	Fab MSL-109 light chain	-	-	-
H	Fab MSL-109 heavy 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
C	IPR012564	Herpesvirus UL74, glycoprotein	Family
D	IPR027290	Platelet-derived growth factor receptor alpha	Family
D	IPR001824	Tyrosine-protein kinase, receptor class III, conserved site	Conserved Site
D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D	IPR008266	Tyrosine-protein kinase, active site	Active Site
D	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
D	IPR000719	Protein kinase domain	Domain
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR007110	Immunoglobulin-like domain	Domain
D	IPR017441	Protein kinase, ATP binding site	Binding Site
D	IPR003599	Immunoglobulin subtype	Domain
D	IPR003598	Immunoglobulin subtype 2	Domain
D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
D	IPR013098	Immunoglobulin I-set	Domain
D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D	Pharos: P16234	gastrointestinal stromal tumor medulloblastoma hypereosinophilic syndrome mesenchymal chondrosarcoma cleft palate melanotic medulloblastoma Fetal Death adult medulloblastoma cancer medullomyoblastoma with myogenic differentiation idiopathic hypereosinophilic syndrome glioblastoma childhood medulloblastoma spina bifida ulcerative colitis gastrointestinal stromal tumor medulloblastoma hypereosinophilic syndrome mesenchymal chondrosarcoma cleft palate melanotic medulloblastoma Fetal Death adult medulloblastoma cancer medullomyoblastoma with myogenic differentiation idiopathic hypereosinophilic syndrome glioblastoma childhood medulloblastoma spina bifida ulcerative colitis cutaneous melanoma desmoplastic/nodular medulloblastoma ductal breast carcinoma in situ myeloid neoplasm associated with PDGFRA rearrangement oligodendroglioma acute lymphoblastic leukemia pancreatic ductal adenocarcinoma breast cancer renal cell carcinoma large cell medulloblastoma chronic eosinophilic leukemia lung adenocarcinoma lung disease thyroid gland follicular carcinoma corneal disease malignant mesothelioma uterine corpus leiomyoma cystic fibrosis digestive system disease Emery-Dreifuss muscular dystrophy fetal alcohol spectrum disorder osteosarcoma adrenal cortex adenoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma astrocytic tumor psoriasis breast carcinoma interstitial lung disease Carney-Stratakis syndrome Sjogren syndrome lung cancer tethered spinal cord syndrome congenital anemia thyroid gland papillary carcinoma malignant pancreatic neoplasm melanoma Duchenne muscular dystrophy metastatic melanoma endometrial carcinoma non-small cell lung carcinoma fetal alcohol syndrome ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm pituitary cancer atopic eczema idiopathic pulmonary fibrosis Burkitt lymphoma invasive ductal breast carcinoma sarcoma lung carcinoma thymic carcinoma congestive heart failure malignant colon neoplasm

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.