5C6T | pdb_00005c6t

Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.260 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody.

Chandramouli, S.Ciferri, C.Nikitin, P.A.Calo, S.Gerrein, R.Balabanis, K.Monroe, J.Hebner, C.Lilja, A.E.Settembre, E.C.Carfi, A.

(2015) Nat Commun 6: 8176-8176

  • DOI: https://doi.org/10.1038/ncomms9176
  • Primary Citation Related Structures: 
    5C6T

  • PubMed Abstract: 

    Human cytomegalovirus (HCMV) poses a significant threat to immunocompromised individuals and neonates infected in utero. Glycoprotein B (gB), the herpesvirus fusion protein, is a target for neutralizing antibodies and a vaccine candidate due to its indispensable role in infection. Here we show the crystal structure of the HCMV gB ectodomain bound to the Fab fragment of 1G2, a neutralizing human monoclonal antibody isolated from a seropositive subject. The gB/1G2 interaction is dominated by aromatic residues in the 1G2 heavy chain CDR3 protruding into a hydrophobic cleft in the gB antigenic domain 5 (AD-5). Structural analysis and comparison with HSV gB suggest the location of additional neutralizing antibody binding sites on HCMV gB. Finally, immunoprecipitation experiments reveal that 1G2 can bind to HCMV virion gB suggesting that its epitope is exposed and accessible on the virus surface. Our data will support the development of vaccines and therapeutic antibodies against HCMV infection.


  • Organizational Affiliation
    • GSK Vaccines, 45 Sidney Street, Cambridge, Massachusetts 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 123.41 kDa 
  • Atom Count: 6,411 
  • Modeled Residue Count: 783 
  • Deposited Residue Count: 1,083 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein B636Human herpesvirus 5 strain TowneMutation(s): 7 
Gene Names: gBUL55
UniProt
Find proteins for P13201 (Human cytomegalovirus (strain Towne))
Explore P13201 
Go to UniProtKB:  P13201
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13201
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
1G2 Fab heavy chainB [auth H]233Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
1G2 Fab light chainC [auth L]214Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
M [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.260 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.486α = 90
b = 176.486β = 90
c = 176.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-06
    Changes: Structure summary