7LBF | pdb_00007lbf

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	Herpes_glycoH_C	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: Herpes_glycoH_C	ECOD (1.6)
A	Herpes_glycop_H	e7lbfA1	A: a+b complex topology	X: gH main domain (From Topology)	H: gH main domain (From Topology)	T: gH main domain	F: Herpes_glycop_H	ECOD (1.6)
B	F_UNCLASSIFIED	e7lbfB1	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)
B	F_UNCLASSIFIED	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: F_UNCLASSIFIED	ECOD (1.6)
D	IG_like	e7lbfD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: IG_like	ECOD (1.6)
D	I-set	e7lbfD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set	ECOD (1.6)
D	Ig_2	e7lbfD3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ig_2	ECOD (1.6)
E	V-set	e7lbfE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
F	V-set_8	e7lbfF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
G	V-set	e7lbfG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
H	V-set_12	e7lbfH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	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 (2025-03-21)
F	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2025-03-21)
G	Light Chain	IGKV2	Kappa	envelope glycoprotein h	SAbDab (2025-03-21)
H	Heavy Chain	IGHV3	-	envelope glycoprotein h	SAbDab (2025-03-21)

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	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 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 life cycle 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 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 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	cell periphery cellular anatomical structure plasma membrane membrane 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 cellular anatomical structure plasma membrane membrane 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 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 life cycle 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 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 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	cell periphery cellular anatomical structure plasma membrane membrane 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 cellular anatomical structure plasma membrane membrane 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	molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein ephrin receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transmembrane-ephrin receptor activity protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity collagen receptor activity protein tyrosine kinase collagen receptor activity GPI-linked ephrin receptor activity protein binding binding signaling receptor binding platelet-derived growth factor receptor binding growth factor receptor binding protein-hormone receptor activity insulin receptor activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding platelet-derived growth factor beta-receptor activity platelet-derived growth factor receptor activity stem cell factor receptor activity protein-containing complex binding brain-derived neurotrophic factor receptor activity neurotrophin receptor activity platelet-derived growth factor binding growth factor binding hepatocyte growth factor receptor activity macrophage colony-stimulating factor receptor activity platelet-derived growth factor alpha-receptor activity phosphoric ester hydrolase activity enzyme regulator activity phospholipase C activator activity molecular function activator activity phosphoric diester hydrolase activity hydrolase activity phospholipase activity lipase activity enzyme activator activity hydrolase activity, acting on ester bonds phospholipase activator activity phospholipase C activity molecular function regulator activity lipase activator activity identical protein binding protein homodimerization activity protein dimerization activity vascular endothelial growth factor receptor activity histone H2AXY142 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity histone H3Y41 kinase activity histone H3 kinase activity placental growth factor receptor activity insulin-like growth factor receptor activity boss receptor activity epidermal growth factor receptor activity vascular endothelial growth factor binding fibroblast 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 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 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 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 anatomical structure morphogenesis 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 cell surface receptor signaling pathway platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression signal transduction involved in regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of body fluid levels negative regulation of biological process regulation of cell activation negative regulation of platelet activation regulation of response to wounding regulation of coagulation response to stress regulation of response to stress negative regulation of cellular process coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis wound healing negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis negative regulation of response to wounding blood coagulation 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 platelet activation 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 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 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 cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation 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 cell migration cell motility cellular developmental process cardiac muscle cell development cellular component assembly involved in morphogenesis cell development membraneless organelle assembly 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 cell differentiation 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 regulation of developmental process regulation of cell differentiation stem cell differentiation regulation of stem cell differentiation mesenchymal stem cell differentiation regulation of mesenchymal stem cell differentiation rhythmic process ovulation cycle process gonad development luteinization female gonad development multicellular organismal reproductive process female sex differentiation development of primary female sexual characteristics ovulation cycle development of primary sexual characteristics platelet-derived growth factor receptor-alpha signaling pathway cellular response to growth factor stimulus 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 response to endogenous stimulus vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus response to growth factor homotypic cell-cell adhesion platelet aggregation cell adhesion cell-cell adhesion embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development 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 in utero embryonic development protein phosphorylation protein autophosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process cell chemotaxis cellular response to chemical stimulus cellular response to acid chemical cellular response to amino acid stimulus response to acid chemical response to amino acid fat cell differentiation white fat cell differentiation male gonad development development of primary male sexual characteristics Leydig cell differentiation head development face morphogenesis head morphogenesis face development body morphogenesis odontogenesis of dentin-containing tooth odontogenesis estrogen metabolic process regulation of hormone levels steroid metabolic process hormone metabolic process lipid metabolic process 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 digestive system development embryonic digestive tract morphogenesis digestive tract development digestive tract morphogenesis embryonic digestive tract development hemopoiesis hematopoietic progenitor cell differentiation roof of mouth development	protein-containing complex receptor complex cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle protein-containing complex receptor complex cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane cell surface external side of plasma membrane side of membrane Golgi apparatus 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
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	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
D	IPR000719	Protein kinase domain	Domain
D	IPR003599	Immunoglobulin domain subtype	Domain
D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D	IPR007110	Immunoglobulin-like domain	Domain
D	IPR017441	Protein kinase, ATP binding site	Binding Site
D	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
D	IPR008266	Tyrosine-protein kinase, active site	Active Site
D	IPR003598	Immunoglobulin subtype 2	Domain
D	IPR013098	Immunoglobulin I-set	Domain
D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
D	IPR050122	Receptor Tyrosine Kinase	Family

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 myeloid neoplasm associated with PDGFRA rearrangement ductal breast carcinoma in situ oligodendroglioma pancreatic ductal adenocarcinoma acute lymphoblastic leukemia breast cancer renal cell carcinoma large cell medulloblastoma lung adenocarcinoma chronic eosinophilic leukemia lung disease malignant mesothelioma thyroid gland follicular carcinoma corneal disease uterine corpus leiomyoma cystic fibrosis digestive system disease Emery-Dreifuss muscular dystrophy osteosarcoma fetal alcohol spectrum disorder pancreatic intraductal papillary-mucinous carcinoma adrenal cortex adenoma pilocytic astrocytoma astrocytic tumor psoriasis breast carcinoma interstitial lung disease Carney-Stratakis syndrome lung cancer Sjogren syndrome tethered spinal cord syndrome congenital anemia malignant pancreatic neoplasm thyroid gland papillary carcinoma melanoma metastatic melanoma Duchenne muscular dystrophy non-small cell lung carcinoma endometrial carcinoma ovarian cancer fetal alcohol syndrome pancreatic intraductal papillary-mucinous neoplasm adrenal cortex carcinoma pituitary cancer atopic eczema idiopathic pulmonary fibrosis Burkitt lymphoma invasive ductal breast carcinoma sarcoma lung carcinoma malignant colon neoplasm thymic carcinoma congestive heart failure