7T4R | pdb_00007t4r

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)
R	SBP_bac_11	e7t4rR1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
I	PK_C	e7t4rI1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PK_C	ECOD (develop294)
Q	SBP_bac_11	e7t4rQ1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
H	SBP_bac_11	e7t4rH1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
P	SBP_bac_11	e7t4rP1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
G	SBP_bac_11	e7t4rG1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
N	SBP_bac_11	e7t4rN1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
E	SBP_bac_11	e7t4rE1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
M	PK_C	e7t4rM2	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PK_C	ECOD (develop294)
D	SBP_bac_11	e7t4rD1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
L	SBP_bac_11	e7t4rL1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
C	SBP_bac_11	e7t4rC1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
K	SBP_bac_11	e7t4rK1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
B	PK_C	e7t4rB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PK_C	ECOD (develop294)
S	SBP_bac_11	e7t4rS1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: SBP_bac_11	ECOD (develop294)
J	PK_C	e7t4rJ1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PK_C	ECOD (develop294)
A	PK_C	e7t4rA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PK_C	ECOD (develop294)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
I, R	Light Chain	IGKV2	Kappa	envelope glycoprotein h	SAbDab (2026-03-20)
H, Q	Light Chain	IGKV1	Kappa	envelope glycoprotein h	SAbDab (2026-03-20)
G, P	Heavy Chain	IGHV1	-	envelope glycoprotein h	SAbDab (2026-03-20)
J, S	Heavy Chain	IGHV3	-	envelope glycoprotein h	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, N	PF11668	HCMV glycoprotein pUL130 (Gp_UL130)	HCMV glycoprotein pUL130	-	Family
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
A	PF25444	Thrombomodulin-like domain (THBD)	Thrombomodulin-like domain	This domain is found in human Thrombomodulin (THBD) and similar animal proteins. THBD is an endothelial cell receptor that plays a critical role in regulating several physiological processes including hemostasis, coagulation, fibrinolysis, inflammati ...	This domain is found in human Thrombomodulin (THBD) and similar animal proteins. THBD is an endothelial cell receptor that plays a critical role in regulating several physiological processes including hemostasis, coagulation, fibrinolysis, inflammation, and angiogenesis. This domain adopts a mainly beta configuration.	Domain
A	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I, R	Fab MSL-109 light chain	-	-	-
H, Q	Fab 13H11 light chain	-	-	-
G, P	Fab 13H11 heavy chain	-	-	-
F, O	Envelope protein UL131A	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane
E, N	Envelope glycoprotein UL130	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane
D, M	Envelope protein UL128	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane
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 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 other organism part virion membrane 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 other organism part virion membrane host intracellular part host cell cytoplasm host cell Golgi apparatus host intracellular region host cell cytoplasm part
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 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 other organism part virion membrane host intracellular membrane-bounded organelle 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 other organism part 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, S	Fab MSL-109 heavy chain	-	-	-
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 protein maturation blood coagulation, fibrin clot formation protein metabolic process protein activation cascade 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 chemical response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP 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 cellular anatomical structure cell surface membrane plasma membrane 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 cellular anatomical structure cell surface membrane plasma membrane 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, N	IPR021038	Herpesvirus UL130, cytomegalovirus	Family
D, M	IPR057762	UL128-like, Cytomegalovirus	Family
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
A	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
A	IPR052126	Spindle_Organization_and_Thrombomodulin	Family
A	IPR057350	Thrombomodulin-like domain	Domain
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

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 thrombotic disease gastric cancer 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 thrombotic disease gastric cancer 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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.