6BF4

Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.382 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.

Zhou, T.Zheng, A.Baxa, U.Chuang, G.Y.Georgiev, I.S.Kong, R.O'Dell, S.Shahzad-Ul-Hussan, S.Shen, C.H.Tsybovsky, Y.Bailer, R.T.Gift, S.K.Louder, M.K.McKee, K.Rawi, R.Stevenson, C.H.Stewart-Jones, G.B.E.Taft, J.D.Waltari, E.Yang, Y.Zhang, B.Shivatare, S.S.Shivatare, V.S.Lee, C.D.Wu, C.Y.Mullikin, J.C.Bewley, C.A.Burton, D.R.Polonis, V.R.Shapiro, L.Wong, C.H.Mascola, J.R.Kwong, P.D.Wu, X.

(2018) Immunity 48: 500-513.e6

  • DOI: 10.1016/j.immuni.2018.02.013

  • PubMed Abstract: 
  • Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified anti ...

    Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains. The crystal structure of the antigen-binding fragment of VRC-PG05 in complex with gp120 revealed an epitope comprised primarily of N-linked glycans from N262, N295, and N448 at the silent face center. Somatic hypermutation occurred preferentially at antibody residues that interacted with these glycans, suggesting somatic development of glycan recognition. Resistance to VRC-PG05 in donor #74 involved shifting of glycan-N448 to N446 or mutation of glycan-proximal residue E293. HIV-1 neutralization can thus be achieved at the silent face center by glycan-recognizing antibody; along with other known epitopes, the VRC-PG05 epitope completes coverage by neutralizing antibody of all major exposed regions of the prefusion closed trimer.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 clade AE gp120 core
A, G
344N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VRC-PG05 Fab heavy chain
B, H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VRC-PG05 Fab light chain
C, L
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, G
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, G, H, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.382 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 231.438α = 90.00
b = 89.255β = 119.15
c = 123.407γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SERGUIdata collection
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-25 
  • Released Date: 2018-03-07 
  • Deposition Author(s): Zhou, T., Kwong, P.D.

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references, Derived calculations, Structure summary