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: 2.80 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 

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 U S A 106: 14751-14756

  • DOI: 10.1073/pnas.0902663106
  • Primary Citation of Related Structures:  
    3F50, 3G7A, 3F4Y, 3F4Z

  • 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 context o ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoprotein gp160 A36N/AMutation(s): 0 
Find proteins for P04580 (Human immunodeficiency virus type 1 group M subtype D (isolate Z6))
Explore P04580 
Go to UniProtKB:  P04580
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Chimeric alpha+alpha/beta-peptide analogue of the HIV gp41 CHR domain B38N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
B3E
Query on B3E		BL-PEPTIDE LINKINGC6 H11 N O4GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.254 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.043α = 90
b = 57.043β = 90
c = 186.314γ = 120
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
PHASERphasing
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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