1AVZ

V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1AVZ/pdb

• Classification: COMPLEX (MYRISTYLATION/TRANSFERASE)
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-09-23 Released: 1998-03-25 
• Deposition Author(s): Arold, S., Franken, P., Dumas, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.270 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

The crystal structure of HIV-1 Nef protein bound to the Fyn kinase SH3 domain suggests a role for this complex in altered T cell receptor signaling.

Arold, S., Franken, P., Strub, M.P., Hoh, F., Benichou, S., Benarous, R., Dumas, C.

(1997) Structure 5: 1361-1372

• PubMed: 9351809 
• DOI: https://doi.org/10.1016/s0969-2126(97)00286-4
• Primary Citation of Related Structures:  
  1AVV, 1AVZ


• PubMed Abstract: 
  

  Human immunodeficiency virus (HIV) Nef protein accelerates virulent progression of acquired immunodeficiency syndrome (AIDS) by its interaction with specific cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src family of kinases. The structures of free Nef and Nef bound to Src homology region 3 (SH3) domain are important for the elucidation of how the affinity and specificity for the Src kinase family SH3 domains are achieved, and also for the development of potential drugs and vaccines against AIDS.

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Organizational Affiliation: 

Centre de Biochimie Structurale, UMR C9955 CNRS, U414 INSERM, Université Montpellier I, Faculté de Pharmacie, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.66 kDa 
• Atom Count: 2,186 
• Modelled Residue Count: 260 
• Deposited Residue Count: 359 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEGATIVE FACTOR	A, B	151	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: HIV-1 NEF
UniProt
Find proteins for P03406 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03406  Go to UniProtKB:  P03406

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FYN TYROSINE KINASE	C	57	Homo sapiens	Mutation(s): 0  Gene Names: FYN TYROSINE KINASE EC: 2.7.1.112
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens) Explore P06241  Go to UniProtKB:  P06241
PHAROS:  P06241 GTEx:  ENSG00000010810

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.270 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.2	α = 90
b = 108.2	β = 90
c = 223.7	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
XSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-25 
Deposition Author(s): Arold, S., Franken, P., Dumas, C.

Revision History  

• Version 1.0: 1998-03-25
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection, Other
• Version 1.4: 2018-04-11
  Changes: Data collection
• Version 1.5: 2023-08-02
  Changes: Database references, Refinement description