Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41661.51 
• Atom Count: 2186 
• Residue Count: 359 
• Unique protein chains: 2

1AVZ

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

• DOI: 10.2210/pdb1AVZ/pdb

• Classification: COMPLEX (MYRISTYLATION/TRANSFERASE)
• Organism(s): Human immunodeficiency virus type 1 group M subtype B, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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 Å
• R-Value Free: 0.270 
• R-Value Work: 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 
• Primary Citation of Related Structures:  
  1AVV
• Also Cited By: 4D8D


• 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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Related Citations: 

• Crystal Structure of the Conserved Core of HIV-1 Nef Complexed with a Src Family SH3 Domain
  Lee, C.H.,Saksela, K.,Mirza, U.A.,Chait, B.T.,Kuriyan, J.
  (1996) Cell 85: 931
• The Solution Structure of HIV-1 Nef Reveals an Unexpected Fold and Permits Delineation of the Binding Surface for the SH3 Domain of HCK Tyrosine Protein Kinase
  Grzesiek, S.,Bax, A.,Clore, G.M.,Gronenborn, A.M.,Hu, J.S.,Kaufman, J.,Palmer, I.,Stahl, S.J.,Wingfield, P.T.
  (1996) Nat.Struct.Mol.Biol. 3: 340




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEGATIVE FACTOR	A, B	151	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: nef
Find proteins for P03406 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P03406

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
FYN TYROSINE KINASE	C	57	Homo sapiens	Mutation(s): 0  Gene Names: FYN EC: 2.7.10.2
Find proteins for P06241 (Homo sapiens) Go to Gene View: FYN Go to UniProtKB:  P06241

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3 Å
• R-Value Free: 0.270 
• R-Value Work: 0.220 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 108.200	α = 90.00
b = 108.200	β = 90.00
c = 223.700	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-23 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-04
  Type: Data collection, Other
• Version 1.4: 2018-04-11
  Type: Data collection