7T4S

CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with NRP2 and neutralizing fabs 8I21 and 13H11


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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

  • 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein H767Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL75gH
UniProt
Find proteins for Q6SW67 (Human cytomegalovirus (strain Merlin))
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Go to UniProtKB:  Q6SW67
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UniProt GroupQ6SW67
Glycosylation
Glycosylation Sites: 3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein L278Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL115gL
UniProt
Find proteins for F5HCH8 (Human cytomegalovirus (strain Merlin))
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UniProt GroupF5HCH8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein UL128171Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL128
UniProt
Find proteins for V9LLX6 (Human cytomegalovirus (strain Merlin))
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UniProt GroupV9LLX6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glycoprotein UL130254Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL130
UniProt
Find proteins for F5HCP3 (Human cytomegalovirus (strain Merlin))
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UniProt GroupF5HCP3
Glycosylation
Glycosylation Sites: 2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope protein UL131A129Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL131AHHV5wtgp112
UniProt
Find proteins for F5HET4 (Human cytomegalovirus (strain Merlin))
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UniProt GroupF5HET4
Glycosylation
Glycosylation Sites: 1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropilin-2875Homo sapiensMutation(s): 0 
Gene Names: NRP2VEGF165R2
UniProt & NIH Common Fund Data Resources
Find proteins for O60462 (Homo sapiens)
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Go to UniProtKB:  O60462
PHAROS:  O60462
GTEx:  ENSG00000118257 
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UniProt GroupO60462
Glycosylation
Glycosylation Sites: 2Go to GlyGen: O60462-1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 8I21 heavy chainG [auth H]249Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 13H11 heavy chainH [auth J]250Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 13H11 light chainI [auth K]237Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 8I21 light chainJ [auth I]238Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
O [auth D]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth D],
P [auth D],
Q [auth E],
R [auth F],
S [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
T [auth F]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM1.02
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-23
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Refinement description, Structure summary