3G7A

HIV gp41 six-helix bundle composed of a chimeric alpha+alpha/beta-peptide analogue of the CHR domain in complex with an NHR domain alpha-peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers

Horne, W.S.Johnson, L.M.Ketas, T.J.Klasse, P.J.Lu, M.Moore, J.P.Gellman, S.H.

(2009) Proc.Natl.Acad.Sci.USA 106: 14751-14756

  • DOI: 10.1073/pnas.0902663106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining alpha- and beta-amino acid residues in the conte ...

    Unnatural oligomers that can mimic protein surfaces offer a potentially useful strategy for blocking biomedically important protein-protein interactions. Here we evaluate an approach based on combining alpha- and beta-amino acid residues in the context of a polypeptide sequence from the HIV protein gp41, which represents an excellent testbed because of the wealth of available structural and biological information. We show that alpha/beta-peptides can mimic structural and functional properties of a critical gp41 subunit. Physical studies in solution, crystallographic data, and results from cell-fusion and virus-infectivity assays collectively indicate that the gp41-mimetic alpha/beta-peptides effectively block HIV-cell fusion via a mechanism comparable to that of gp41-derived alpha-peptides. An optimized alpha/beta-peptide is far less susceptible to proteolytic degradation than is an analogous alpha-peptide. Our findings show how a two-stage design approach, in which sequence-based alpha-->beta replacements are followed by site-specific backbone rigidification, can lead to physical and biological mimicry of a natural biorecognition process.


    Organizational Affiliation

    Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160
A
36Human immunodeficiency virus type 1 group M subtype D (isolate Z6)Mutation(s): 0 
Gene Names: env
Find proteins for P04580 (Human immunodeficiency virus type 1 group M subtype D (isolate Z6))
Go to UniProtKB:  P04580
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain
B
38N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACE
Query on ACE

Download SDF File 
Download CCD File 
A
ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E
B
L-PEPTIDE LINKINGC6 H11 N O4GLU
XPC
Query on XPC
B
peptide-likeC5 H10 N2 O2

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XCP
Query on XCP
B
peptide-likeC6 H11 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 57.043α = 90.00
b = 57.043β = 90.00
c = 186.314γ = 120.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
PHASERphasing
REFMACrefinement
PROTEUM PLUSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance