6ME1

Crystal structure of the clade B isolate B41 mutant fusion peptide (residues 512-521) in complex with VRC34.01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report



Literature

Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide.

Kumar, S.Sarkar, A.Pugach, P.Sanders, R.W.Moore, J.P.Ward, A.B.Wilson, I.A.

(2019) Nat Commun 10: 763-763

  • DOI: 10.1038/s41467-019-08738-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The N-terminal fusion peptide (FP) of the human immunodeficiency virus (HIV)-1 envelope glycoprotein (Env) gp41 subunit plays a critical role in cell entry. However, capturing the structural flexibility in the unbound FP is challenging in the native ...

    The N-terminal fusion peptide (FP) of the human immunodeficiency virus (HIV)-1 envelope glycoprotein (Env) gp41 subunit plays a critical role in cell entry. However, capturing the structural flexibility in the unbound FP is challenging in the native Env trimer. Here, FP conformational isomerism is observed in two crystal structures of a soluble clade B transmitted/founder virus B41 SOSIP.664 Env with broadly neutralizing antibodies (bNAbs) PGT124 and 35O22 to aid in crystallization and that are not specific for binding to the FP. Large rearrangements in the FP and fusion peptide proximal region occur around M530, which remains anchored in the tryptophan clasp (gp41 W623, W628, W631) in the B41 Env prefusion state. Further, we redesigned the FP at position 518 to reinstate the bNAb VRC34.01 epitope. These findings provide further structural evidence for the dynamic nature of the FP and how a bNAb epitope can be restored during vaccine design.


    Organizational Affiliation

    Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. wilson@scripps.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VRC34.01 Fab light chainB, D212Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Envelope glycoprotein gp160E, F16Human immunodeficiency virus 1Mutation(s): 0 
Find proteins for P03375 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Explore P03375 
Go to UniProtKB:  P03375
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VRC34.01 Fab heavy chainA, C223Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.421α = 90
b = 123.67β = 90.87
c = 101.253γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release