7T4R

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11

PDB DOI: https://doi.org/10.2210/pdb7T4R/pdb
EM Map EMD-25686: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Homo sapiens, Human betaherpesvirus 5
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2021-12-10 Released: 2022-03-23
Deposition Author(s): Kschonsak, M., Johnson, M.C., Schelling, R., Green, E.M., Rouge, L., Ho, H., Patel, N., Kilic, C., Kraft, E., Arthur, C.P., Rohou, A.L., Comps-Agrar, L., Martinez-Martin, N., Perez, L., Payandeh, J., Ciferri, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for HCMV Pentamer receptor recognition and antibody neutralization.

Kschonsak, M., Johnson, M.C., Schelling, R., Green, E.M., Rouge, L., Ho, H., Patel, N., Kilic, C., Kraft, E., Arthur, C.P., Rohou, A.L., Comps-Agrar, L., Martinez-Martin, N., Perez, L., Payandeh, J., Ciferri, C.

(2022) Sci Adv 8: eabm2536-eabm2536

PubMed: 35275719 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abm2536
Primary Citation of Related Structures:
7T4Q, 7T4R, 7T4S

PubMed Abstract:
Human cytomegalovirus (HCMV) represents the viral leading cause of congenital birth defects and uses the gH/gL/UL128-130-131A complex (Pentamer) to enter different cell types, including epithelial and endothelial cells. Upon infection, Pentamer elicits the most potent neutralizing response against HCMV, representing a key vaccine candidate. Despite its relevance, the structural basis for Pentamer receptor recognition and antibody neutralization is largely unknown. Here, we determine the structures of Pentamer bound to neuropilin 2 (NRP2) and a set of potent neutralizing antibodies against HCMV. Moreover, we identify thrombomodulin (THBD) as a functional HCMV receptor and determine the structures of the Pentamer-THBD complex. Unexpectedly, both NRP2 and THBD also promote dimerization of Pentamer. Our results provide a framework for understanding HCMV receptor engagement, cell entry, antibody neutralization, and outline strategies for antiviral therapies against HCMV.

Organizational Affiliation

Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA.

Macromolecule Content

Total Structure Weight: 638.36 kDa
Atom Count: 28,717
Modelled Residue Count: 3,595
Deposited Residue Count: 5,727
Unique protein chains: 10

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombomodulin	A	527	Homo sapiens	Mutation(s): 0 Gene Names: THBD, THRM
UniProt & NIH Common Fund Data Resources
Find proteins for P07204 (Homo sapiens) Explore P07204 Go to UniProtKB: P07204
PHAROS: P07204 GTEx: ENSG00000178726
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07204
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	B, K	767	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: UL75, gH
UniProt
Find proteins for Q6SW67 (Human cytomegalovirus (strain Merlin)) Explore Q6SW67 Go to UniProtKB: Q6SW67
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UniProt Group	Q6SW67
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	C, L	278	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: UL115, gL
UniProt
Find proteins for F5HCH8 (Human cytomegalovirus (strain Merlin)) Explore F5HCH8 Go to UniProtKB: F5HCH8
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UniProt Group	F5HCH8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein UL128	D, M	171	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: UL128
UniProt
Find proteins for V9LLX6 (Human cytomegalovirus (strain Merlin)) Explore V9LLX6 Go to UniProtKB: V9LLX6
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UniProt Group	V9LLX6
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein UL130	E, N	254	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: UL130
UniProt
Find proteins for F5HCP3 (Human cytomegalovirus (strain Merlin)) Explore F5HCP3 Go to UniProtKB: F5HCP3
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UniProt Group	F5HCP3
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein UL131A	F, O	129	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: UL131A, HHV5wtgp112
UniProt
Find proteins for F5HET4 (Human cytomegalovirus (strain Merlin)) Explore F5HET4 Go to UniProtKB: F5HET4
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UniProt Group	F5HET4
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 13H11 heavy chain	G, P	250	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 13H11 light chain	H, Q	237	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MSL-109 light chain	I, R	257	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MSL-109 heavy chain	J, S	257	Homo sapiens	Mutation(s): 0
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain BA [auth K] SDF format, chain CA [auth K] SDF format, chain DA [auth K] SDF format, chain EA [auth K] SDF format, chain FA [auth N] SDF format, chain GA [auth O] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth E] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth K] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth O] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth E]	AA [auth K] BA [auth K] CA [auth K] DA [auth K] EA [auth K] AA [auth K], BA [auth K], CA [auth K], DA [auth K], EA [auth K], FA [auth N], GA [auth O], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth C], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth K] Focus chain BA [auth K] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth K] Focus chain CA [auth K] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth N] Focus chain GA [auth O] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth E]