7M22 | pdb_00007m22

Cryo-EM structure of the HCMV pentamer bound by human neuropilin 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7M22

This is version 1.2 of the entry. See complete history

Literature

Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies.

Wrapp, D.Ye, X.Ku, Z.Su, H.Jones, H.G.Wang, N.Mishra, A.K.Freed, D.C.Li, F.Tang, A.Li, L.Jaijyan, D.K.Zhu, H.Wang, D.Fu, T.M.Zhang, N.An, Z.McLellan, J.S.

(2022) Sci Adv 8: eabm2546-eabm2546

  • DOI: https://doi.org/10.1126/sciadv.abm2546
  • Primary Citation Related Structures: 
    7KBA, 7KBB, 7LYV, 7LYW, 7M1C, 7M22, 7M30

  • PubMed Abstract: 

    Human cytomegalovirus (HCMV) encodes multiple surface glycoprotein complexes to infect a variety of cell types. The HCMV Pentamer, composed of gH, gL, UL128, UL130, and UL131A, enhances entry into epithelial, endothelial, and myeloid cells by interacting with the cell surface receptor neuropilin 2 (NRP2). Despite the critical nature of this interaction, the molecular determinants that govern NRP2 recognition remain unclear. Here, we describe the cryo-EM structure of NRP2 bound to Pentamer. The high-affinity interaction between these proteins is calcium dependent and differs from the canonical carboxyl-terminal arginine (CendR) binding that NRP2 typically uses. We also determine the structures of four neutralizing human antibodies bound to the HCMV Pentamer to define susceptible epitopes. Two of these antibodies compete with NRP2 binding, but the two most potent antibodies recognize a previously unidentified epitope that does not overlap the NRP2-binding site. Collectively, these findings provide a structural basis for HCMV tropism and antibody-mediated neutralization.


  • Organizational Affiliation
    • Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 117.36 kDa 
  • Atom Count: 6,042 
  • Modeled Residue Count: 748 
  • Deposited Residue Count: 1,025 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein UL128A [auth C]144Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL128
UniProt
Find proteins for P16837 (Human cytomegalovirus (strain AD169))
Explore P16837 
Go to UniProtKB:  P16837
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16837
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein UL130B [auth D]189Human betaherpesvirus 5Mutation(s): 0 
Gene Names: UL130
UniProt
Find proteins for P16772 (Human cytomegalovirus (strain AD169))
Explore P16772 
Go to UniProtKB:  P16772
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16772
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
UL131AC [auth E]111Human betaherpesvirus 5Mutation(s): 0 
UniProt
Find proteins for F5HET4 (Human cytomegalovirus (strain Merlin))
Explore F5HET4 
Go to UniProtKB:  F5HET4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF5HET4
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuropilin-2D [auth N]581Homo sapiensMutation(s): 0 
Gene Names: NRP2VEGF165R2
UniProt & NIH Common Fund Data Resources
Find proteins for O60462 (Homo sapiens)
Explore O60462 
Go to UniProtKB:  O60462
PHAROS:  O60462
GTEx:  ENSG00000118257 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60462
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O60462-1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary