4ORZ

HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the inhibition of HIV-1 Nef by a high-affinity binding single-domain antibody.

Lulf, S.Matz, J.Rouyez, M.C.Jarviluoma, A.Saksela, K.Benichou, S.Geyer, M.

(2014) Retrovirology 11: 24-24

  • DOI: 10.1186/1742-4690-11-24

  • PubMed Abstract: 
  • The HIV-1 Nef protein is essential for AIDS pathogenesis by its interaction with host cell surface receptors and signaling factors. Despite its critical role as a virulence factor Nef is not targeted by current antiviral strategies.

    The HIV-1 Nef protein is essential for AIDS pathogenesis by its interaction with host cell surface receptors and signaling factors. Despite its critical role as a virulence factor Nef is not targeted by current antiviral strategies.


    Organizational Affiliation

    Center of Advanced European Studies and Research, Group Physical Biochemistry, Bonn, Germany. matthias.geyer@caesar.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase HCK
A
67Homo sapiensMutation(s): 6 
Gene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Go to Gene View: HCK
Go to UniProtKB:  P08631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
B
145Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)Mutation(s): 4 
Gene Names: nef
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Go to UniProtKB:  P03407
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
single domain antibody sdAb19
C
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 73.000α = 90.00
b = 73.000β = 90.00
c = 71.000γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
ADSCdata collection
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-12 
  • Released Date: 2014-03-26 
  • Deposition Author(s): Geyer, M., Lulf, S.

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release