4RQS

Crystal structure of fully glycosylated HIV-1 gp120 core bound to CD4 and 17b Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.493 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262.

Kong, L.Wilson, I.A.Kwong, P.D.

(2015) Proteins 83: 590-596

  • DOI: 10.1002/prot.24747

  • PubMed Abstract: 
  • The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensi ...

    The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc(2)Man(7) was modeled. The GlcNAc stem of this glycan is largely buried in a cleft in gp120, suggesting a role in gp120 folding and stability. Its arms interact with the stems of neighboring glycans from the oligomannose patch, which is a major target for broadly neutralizing antibodies.


    Organizational Affiliation

    Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, 20892; Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, the Scripps Research Institute, La Jolla, California; Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, the Scripps Research Institute, La Jolla, California.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-domain CD4
B
185Homo sapiensMutation(s): 0 
Gene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
17b Fab Light Chain
C
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
17b Fab Heavy Chain
D
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HIV-1 YU2 gp120 core chimeric protein
G
313Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P35961
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

Download SDF File 
Download CCD File 
G
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.493 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.276 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 171.318α = 90.00
b = 171.318β = 90.00
c = 151.857γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Blu-Icedata collection
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Database references
  • Version 1.3: 2017-06-28
    Type: Source and taxonomy