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: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4ORZ

  • 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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCKA67Homo sapiensMutation(s): 6 
Gene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
NIH Common Fund Data Resources
PHAROS  P08631
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NefB145HIV-1 M:B_ARV2/SF2Mutation(s): 4 
Gene Names: nef
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03407 
Go to UniProtKB:  P03407
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
single domain antibody sdAb19C120Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73α = 90
b = 73β = 90
c = 71γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



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