7M30 | pdb_00007m30

Cryo-EM structure of the HCMV pentamer bound by antibodies 1-103, 1-32 and 2-25


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7M30

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: 224.41 kDa 
  • Atom Count: 9,191 
  • Modeled Residue Count: 1,167 
  • Deposited Residue Count: 2,034 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein LA [auth B]248Human betaherpesvirus 5Mutation(s): 0 
Gene Names: gLUL115
UniProt
Find proteins for P16832 (Human cytomegalovirus (strain AD169))
Explore P16832 
Go to UniProtKB:  P16832
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16832
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope protein UL128B [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
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein UL130C [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
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UL131AD [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
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
2-25 Fab Heavy ChainE [auth F]234Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
2-25 Fab Light ChainF [auth G]212Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
1-32 Fab Heavy ChainG [auth H]241Homo sapiensMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
1-32 Fab Light ChainH [auth L]213Homo sapiensMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
1-103 Fab Heavy ChainI [auth M]232Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
1-103 Fab Light ChainJ [auth N]210Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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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: 2024-11-13
    Changes: Data collection, Structure summary