1G9N

HIV-1 YU2 GP120 ENVELOPE GLYCOPROTEIN COMPLEXED WITH CD4 AND INDUCED NEUTRALIZING ANTIBODY 17B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.

Kwong, P.D.Wyatt, R.Majeed, S.Robinson, J.Sweet, R.W.Sodroski, J.Hendrickson, W.A.

(2000) Structure Fold.Des. 8: 1329-1339

  • Primary Citation of Related Structures:  1G9M

  • PubMed Abstract: 
  • The gp120 exterior envelope glycoprotein of HIV-1 binds sequentially to CD4 and chemokine receptors on cells to initiate virus entry. During natural infection, gp120 is a primary target of the humoral immune response, and it has evolved to resist ant ...

    The gp120 exterior envelope glycoprotein of HIV-1 binds sequentially to CD4 and chemokine receptors on cells to initiate virus entry. During natural infection, gp120 is a primary target of the humoral immune response, and it has evolved to resist antibody-mediated neutralization. We previously reported the structure at 2.5 A of a gp120 core from the HXBc2 laboratory-adapted isolate in complex with a 2 domain fragment of CD4 and the antigen binding fragment of a human antibody. This revealed atomic details of gp120-receptor interactions and suggested multiple mechanisms of immune evasion.


    Related Citations: 
    • Structure of an HIV GP120 Envelope Glycoprotein in Complex with the CD4 Receptor and a Neutralizing Human Antibody
      Kwong, P.D.,Wyatt, R.,Robinson, J.,Sweet, R.W.,Sodroski, J.,Hendrickson, W.A.
      (1998) Nature 393: 648


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENVELOPE GLYCOPROTEIN GP120
G
313Human immunodeficiency virus type 1 group M subtype BGene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P35961
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
T-CELL SURFACE GLYCOPROTEIN CD4
C
185Homo sapiensGene Names: CD4
Find proteins for P01730 (Homo sapiens)
Go to Gene View: CD4
Go to UniProtKB:  P01730
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY 17B, LIGHT CHAIN
L
214N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY 17B, HEAVY CHAIN
H
229N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
G
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-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: 2.9 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 174.980α = 90.00
b = 81.710β = 90.37
c = 74.480γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-27
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-08-02
    Type: Advisory, Refinement description, Source and taxonomy