5C6T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/ncomms9176

  • 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 i ...

    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.,GSK Vaccines, Via Fiorentina 1, Siena 53100, Italy.,Novartis Influenza Vaccines, 45 Sidney Street, Cambridge, Massachusetts 02139, USA.,Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein B
A
636Human cytomegalovirus (strain Towne)Mutation(s): 7 
Gene Names: gB
Find proteins for P13201 (Human cytomegalovirus (strain Towne))
Go to UniProtKB:  P13201
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
1G2 Fab heavy chain
H
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
1G2 Fab light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 176.486α = 90.00
b = 176.486β = 90.00
c = 176.486γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Author supporting evidence, Derived calculations