7T4R

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 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	PF00059	e7t4rA1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
C	PF01801	e7t4rC2	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF01801	ECOD (1.6)
C	PF01801	e7t4rC1	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)
L	PF01801	e7t4rL2	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF01801	ECOD (1.6)
L	PF01801	e7t4rL1	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)
F	F_UNCLASSIFIED	e7t4rF1	A: beta barrels	X: UL131A-like	H: UL131A (From Topology)	T: UL131A	F: F_UNCLASSIFIED	ECOD (1.6)
O	F_UNCLASSIFIED	e7t4rO1	A: beta barrels	X: UL131A-like	H: UL131A (From Topology)	T: UL131A	F: F_UNCLASSIFIED	ECOD (1.6)
H	PF07686	e7t4rH1	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)
Q	PF07686	e7t4rQ1	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)
J	PF07686	e7t4rJ1	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)
S	PF07686	e7t4rS1	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	PF17488	e7t4rB2	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)
B	PF02489	e7t4rB1	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)
K	PF17488	e7t4rK1	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)
K	PF02489	e7t4rK2	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)
D	F_UNCLASSIFIED	e7t4rD1	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)
D	F_UNCLASSIFIED	e7t4rD2	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)
M	F_UNCLASSIFIED	e7t4rM2	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)
M	F_UNCLASSIFIED	e7t4rM1	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)
E	PF11668	e7t4rE2	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF11668	ECOD (1.6)
E	PF11668	e7t4rE1	A: beta barrels	X: UL131A-like	H: UL130 C-terminal domain (From Topology)	T: UL130 C-terminal domain	F: PF11668	ECOD (1.6)
N	PF11668	e7t4rN1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: chemokine-related domain in glycoprotein L (gL)	F: PF11668	ECOD (1.6)
N	PF11668	e7t4rN2	A: beta barrels	X: UL131A-like	H: UL130 C-terminal domain (From Topology)	T: UL130 C-terminal domain	F: PF11668	ECOD (1.6)
G	PF07686	e7t4rG1	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)
P	PF07686	e7t4rP1	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	PF07686	e7t4rI1	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)
R	PF07686	e7t4rR1	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
H, Q	Light Chain	IGKV1	Kappa	envelope glycoprotein h	SAbDab (2024-05-03)
J, S	Heavy Chain	IGHV3	-	envelope glycoprotein h	SAbDab (2024-05-03)
G, P	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2024-05-03)
I, R	Light Chain	IGKV2	Kappa	envelope glycoprotein h	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain
C, L	PF01801	Cytomegalovirus glycoprotein L (Cytomega_gL)	Cytomegalovirus glycoprotein L	-	Family
B, K	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
B, K	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
E, N	PF11668	HCMV glycoprotein pUL130 (Gp_UL130)	HCMV glycoprotein pUL130	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Thrombomodulin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity transmembrane signaling receptor activity	multicellular organismal process regulation of body fluid levels regulation of cellular process response to stimulus regulation of response to external stimulus 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 multicellular organismal process regulation of body fluid levels regulation of cellular process response to stimulus regulation of response to external stimulus 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 regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation biological regulation hemostasis cell activation response to external stimulus 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 regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing cellular process negative regulation of multicellular organismal process platelet activation multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process blood coagulation, common pathway cellular biosynthetic process protein maturation organic substance metabolic process blood coagulation, fibrin clot formation organic substance biosynthetic process protein metabolic process protein activation cascade organonitrogen compound metabolic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process biosynthetic process metabolic process macromolecule metabolic process response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus positive regulation of coagulation positive regulation of biological process positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing fibrinolysis regulation of fibrinolysis positive regulation of multicellular organismal process negative regulation of fibrinolysis response to organic substance response to chemical response to organonitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP response to organic cyclic compound proteolysis zymogen activation protein processing biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane apicolateral plasma membrane plasma membrane region protein-containing complex catalytic complex peptidase complex endopeptidase complex serine-type endopeptidase complex cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane apicolateral plasma membrane plasma membrane region protein-containing complex catalytic complex peptidase complex endopeptidase complex serine-type endopeptidase complex serine-type peptidase complex vacuolar membrane membrane-bounded organelle intracellular anatomical structure vacuole intracellular membrane-bounded organelle intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane extracellular region extracellular space
C, L	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
F, O	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
H, Q	Fab 13H11 light chain	-	-	-
J, S	Fab MSL-109 heavy chain	-	-	-
B, K	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
D, M	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
E, N	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
G, P	Fab 13H11 heavy chain	-	-	-
I, R	Fab MSL-109 light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016187	C-type lectin fold	Homologous Superfamily
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR026823	Complement Clr-like EGF domain	Domain
A	IPR001304	C-type lectin-like	Domain
A	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
A	IPR000742	EGF-like domain	Domain
A	IPR015149	Thrombomodulin-like, EGF-like	Domain
A	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
C, L	IPR002689	Cytomegalovirus glycoprotein L	Family
B, K	IPR038172	Herpesvirus glycoprotein H, C-terminal domain superfamily	Homologous Superfamily
B, K	IPR003493	Herpesvirus glycoprotein H	Family
B, K	IPR035305	Herpesvirus glycoprotein H, C-terminal	Domain
E, N	IPR021038	Herpesvirus UL130, cytomegalovirus	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P07204	thrombophilia atypical hemolytic-uremic syndrome thrombomodulin-related bleeding disorder thrombotic thrombocytopenic purpura acute promyelocytic leukemia adult acute respiratory distress syndrome pulmonary embolism myocardial infarction hemolytic-uremic syndrome neuropathy, painful disseminated intravascular coagulation Liver Cirrhosis, Experimental atypical hemolytic-uremic syndrome with thrombomodulin anomaly gastric cancer thrombotic disease thrombophilia atypical hemolytic-uremic syndrome thrombomodulin-related bleeding disorder thrombotic thrombocytopenic purpura acute promyelocytic leukemia adult acute respiratory distress syndrome pulmonary embolism myocardial infarction hemolytic-uremic syndrome neuropathy, painful disseminated intravascular coagulation Liver Cirrhosis, Experimental atypical hemolytic-uremic syndrome with thrombomodulin anomaly gastric cancer thrombotic disease vascular disease interstitial cystitis lung cancer pancreatic intraductal papillary-mucinous carcinoma breast carcinoma psoriasis hemolytic anemia hereditary diffuse gastric adenocarcinoma lung carcinoma adenoma medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia congenital thrombotic thrombocytopenic purpura ulcerative colitis lung adenocarcinoma adrenal cortex carcinoma ovarian cancer breast cancer pituitary cancer cystic fibrosis gastric neoplasm