3TGS

Crystal structure of HIV-1 clade C strain C1086 gp120 core in complex with NBD-556


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.

Kwon, Y.D.Finzi, A.Wu, X.Dogo-Isonagie, C.Lee, L.K.Moore, L.R.Schmidt, S.D.Stuckey, J.Yang, Y.Zhou, T.Zhu, J.Vicic, D.A.Debnath, A.K.Shapiro, L.Bewley, C.A.Mascola, J.R.Sodroski, J.G.Kwong, P.D.

(2012) Proc.Natl.Acad.Sci.USA 109: 5663-5668

  • DOI: 10.1073/pnas.1112391109
  • Primary Citation of Related Structures:  3TGQ, 3TGR, 3TGT, 3TIH

  • PubMed Abstract: 
  • The HIV-1 envelope (Env) spike (gp120(3)/gp41(3)) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation ...

    The HIV-1 envelope (Env) spike (gp120(3)/gp41(3)) undergoes considerable structural rearrangements to mediate virus entry into cells and to evade the host immune response. Engagement of CD4, the primary human receptor, fixes a particular conformation and primes Env for entry. The CD4-bound state, however, is prone to spontaneous inactivation and susceptible to antibody neutralization. How does unliganded HIV-1 maintain CD4-binding capacity and regulate transitions to the CD4-bound state? To define this mechanistically, we determined crystal structures of unliganded core gp120 from HIV-1 clades B, C, and E. Notably, all of these unliganded HIV-1 structures resembled the CD4-bound state. Conformational fixation with ligand selection and thermodynamic analysis of full-length and core gp120 interactions revealed that the tendency of HIV-1 gp120 to adopt the CD4-bound conformation was restrained by the V1/V2- and V3-variable loops. In parallel, we determined the structure of core gp120 in complex with the small molecule, NBD-556, which specifically recognizes the CD4-bound conformation of gp120. Neutralization by NBD-556 indicated that Env spikes on primary isolates rarely assume the CD4-bound conformation spontaneously, although they could do so when quaternary restraints were loosened. Together, the results suggest that the CD4-bound conformation represents a "ground state" for the gp120 core, with variable loop and quaternary interactions restraining unliganded gp120 from "snapping" into this conformation. A mechanism of control involving deformations in unliganded structure from a functionally critical state (e.g., the CD4-bound state) provides advantages in terms of HIV-1 Env structural diversity and resistance to antibodies and inhibitors, while maintaining elements essential for entry.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 clade C1086 gp120 core
A, B
358Human immunodeficiency virus 1Gene Names: env
Find proteins for C6G099 (Human immunodeficiency virus 1)
Go to UniProtKB:  C6G099
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
03G
Query on 03G

Download SDF File 
Download CCD File 
A, B
N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide
NBD-556
C17 H24 Cl N3 O2
ZKXLQCIOURANAD-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
03GKd: 4100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.960α = 90.00
b = 126.000β = 90.00
c = 191.480γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-05-23
    Type: Database references
  • Version 1.2: 2014-12-17
    Type: Non-polymer description
  • Version 1.3: 2017-11-08
    Type: Refinement description