3AHA

Crystal structure of the complex between gp41 fragments N36 and C34 mutant N126K/E137Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the gp41 amino terminal heptad repeat.

Izumi, K.Nakamura, S.Nakano, H.Shimura, K.Sakagami, Y.Oishi, S.Uchiyama, S.Ohkubo, T.Kobayashi, Y.Fujii, N.Matsuoka, M.Kodama, E.N.

(2010) Antiviral Res. --: --

  • DOI: 10.1016/j.antiviral.2010.04.011

  • PubMed Abstract: 
  • A transmembrane glycoprotein of HIV-1, gp41, plays a central role in membrane fusion of HIV-1 and host cells. Peptides derived from the amino- and carboxyl-terminal heptad repeat (N-HR and C-HR, respectively) of gp41 inhibit this fusion. The mechanis ...

    A transmembrane glycoprotein of HIV-1, gp41, plays a central role in membrane fusion of HIV-1 and host cells. Peptides derived from the amino- and carboxyl-terminal heptad repeat (N-HR and C-HR, respectively) of gp41 inhibit this fusion. The mechanism of resistance to enfuvirtide, a C-HR-derived peptide, is well defined; however the mechanism of resistance to N-HR-derived peptides remains unclear. We characterized an HIV-1 isolate resistant to the N-HR-derived peptide, N36. This HIV-1 acquired a total of four amino acid substitutions, D36G, N126K and E137Q in gp41, and P183Q in gp120. Among these substitutions, N126K and/or E137Q conferred resistance to not only N36, but also C34, which is the corresponding C-HR-derived peptide fusion inhibitor. We performed crystallographic and biochemical analysis of the 6-helix bundle formed by synthetic gp41-derived peptides containing the N126K/E137Q substitutions. The structure of the 6-helix bundle with N126K/E137Q was identical to that in wild-type HIV-1 except for the presence of a new hydrogen bond. Denaturing experiments revealed that the stability of the 6-helix bundle of N126K/E137Q is greater than in the wild-type. These results suggest that the stabilizing effect of N126K/E137Q provides resistance to N36 and C34.


    Organizational Affiliation

    Laboratory of Virus Control, Institute for Virus Research, Kyoto University, 53 Kawaramachi Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transmembrane protein gp41
A, C, E
38Human immunodeficiency virus type 1 group M subtype B (isolate LW123)Mutation(s): 0 
Gene Names: env
Find proteins for Q70626 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123))
Go to UniProtKB:  Q70626
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transmembrane protein gp41
B, D, F
36Human immunodeficiency virus type 1 group M subtype B (isolate LW123)Mutation(s): 2 
Gene Names: env
Find proteins for Q70626 (Human immunodeficiency virus type 1 group M subtype B (isolate LW123))
Go to UniProtKB:  Q70626
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B, C, D, E, F
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B, C, D, E, F
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.632α = 90.00
b = 50.479β = 90.88
c = 56.154γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrystalCleardata collection
CrystalCleardata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance