1AI1

HIV-1 V3 LOOP MIMIC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based design of a constrained peptide mimic of the HIV-1 V3 loop neutralization site.

Ghiara, J.B.Ferguson, D.C.Satterthwait, A.C.Dyson, H.J.Wilson, I.A.

(1997) J.Mol.Biol. 266: 31-39

  • DOI: 10.1006/jmbi.1996.0768

  • PubMed Abstract: 
  • Antigenic variation among different HIV-1 isolates has been a major problem in the development of an effective vaccine against AIDS. Peptide vaccines incorporating structural elements common to groups of viral isolates, such as the clade subtypes of ...

    Antigenic variation among different HIV-1 isolates has been a major problem in the development of an effective vaccine against AIDS. Peptide vaccines incorporating structural elements common to groups of viral isolates, such as the clade subtypes of HIV-1, hold promise; however, the design of such immunogens has been hampered by the lack of specific structural information on the viral proteins to be targeted. As part of a structure-based approach to this problem, we report the design and characterization of a conformationally restricted peptide analog (Aib142) of a highly conserved HIV-1 clade-B sequence from the third variable loop of the membrane glycoprotein gp120. The design strategy incorporates peptide conformational data derived from crystal structure analysis of an MN-isolate peptide (RP142) in complex with the Fab fragment (Fab59.1) of a broadly neutralizing antibody. The synthetic peptide (Aib142) replaces an alanine residue within the V3 loop epitope sequence GPGRAF by the conformationally restricted helicogenic alpha-aminoisobutyryl residue. As expected, the crystal structure of the Fab 59.1-Aib142 complex at 2.8 A resolution shows that the peptide interacts very similarly with the neutralizing antibody. Proton nuclear magnetic resonance (NMR) studies indicate that the free Aib142 peptide is indeed more ordered in solution with a conformational preference that corresponds to the X-ray structure of its Fab-bound form. Aib142 thus represents the first step in the design of conformationally constrained peptide analogs built to mimic biologically relevant structural forms of HIV-1 neutralization sites.


    Organizational Affiliation

    Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA 59.1 FAB (LIGHT CHAIN)
L
215Mus musculusMutation(s): 0 
Gene Names: Igkc
Find proteins for P01837 (Mus musculus)
Go to UniProtKB:  P01837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA 59.1 FAB (HEAVY CHAIN)
H
221Mus musculusMutation(s): 0 
Gene Names: Ighg1 (Igh-4)
Find proteins for P01868 (Mus musculus)
Go to UniProtKB:  P01868
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AIB142
P
24Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: env
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P05877
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AIB
Query on AIB
P
L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Work: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 89.930α = 90.00
b = 154.430β = 90.00
c = 121.460γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
MOSFLMdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-05-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance