4NGH

Crystal structure of the HIV-1 neutralizing antibody 4E10 Fab fragment in complex with a hydrocarbon-stapled peptide containing the 4e10 epitope on gp41 and a tethered phosphate moiety.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Stapled HIV-1 peptides recapitulate antigenic structures and engage broadly neutralizing antibodies.

Bird, G.H.Irimia, A.Ofek, G.Kwong, P.D.Wilson, I.A.Walensky, L.D.

(2014) Nat Struct Mol Biol 21: 1058-1067

  • DOI: 10.1038/nsmb.2922
  • Primary Citation of Related Structures:  
    4NGH, 4NHC

  • PubMed Abstract: 
  • Hydrocarbon stapling can restore bioactive α-helical structure to natural peptides, yielding research tools and prototype therapeutics to dissect and target protein interactions. Here we explore the capacity of peptide stapling to generate high-fidel ...

    Hydrocarbon stapling can restore bioactive α-helical structure to natural peptides, yielding research tools and prototype therapeutics to dissect and target protein interactions. Here we explore the capacity of peptide stapling to generate high-fidelity, protease-resistant mimics of antigenic structures for vaccine development. HIV-1 has been refractory to vaccine technologies thus far, although select human antibodies can broadly neutralize HIV-1 by targeting sequences of the gp41 juxtamembrane fusion apparatus. To develop candidate HIV-1 immunogens, we generated and characterized stabilized α-helices of the membrane-proximal external region (SAH-MPER) of gp41. SAH-MPER peptides were remarkably protease resistant and bound to the broadly neutralizing 4E10 and 10E8 antibodies with high affinity, recapitulating the structure of the MPER epitope when differentially engaged by the two anti-HIV Fabs. Thus, stapled peptides may provide a new opportunity to develop chemically stabilized antigens for vaccination.


    Organizational Affiliation

    1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA. [2] Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FAB LIGHT CHAINL215Homo sapiensMutation(s): 0 
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FAB HEAVY CHAINH228Homo sapiensMutation(s): 0 
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
MODIFIED FRAGMENT OF HIV GLYCOPROTEIN (GP41)P17N/AMutation(s): 0 
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MK8
Query on MK8
PL-PEPTIDE LINKINGC7 H15 N O2LEU
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001208
Query on PRD_001208
PStapled peptide (ACE)NWFNITN(DIV)LW(MK8)I(LYV)KKKPeptide-like /  Unknown

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 226.51α = 90
b = 226.51β = 90
c = 42.33γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references