Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49427.04 
• Atom Count: 2643 
• Residue Count: 422 
• Unique protein chains: 2

1EFN

HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN

• DOI: 10.2210/pdb1EFN/pdb

• Classification: COMPLEX (SH3 DOMAIN/VIRAL ENHANCER)
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI), Homo sapiens
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): 2 


• Deposited: 1996-06-29 Released: 1997-01-11 
• Deposition Author(s): Lee, C.-H., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.215 

Literature

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: 931-942

• PubMed: 8681387 
• Also Cited By: 4D8D


• PubMed Abstract: 
  

The crystal structure of the conserved core of HIV-1 Nef has been determined in complex with the SH3 domain of a mutant Fyn tyrosine kinase (a single amino acid substitution, Arg-96 to isoleucine), to which Nef binds tightly. The conserved PxxP sequence motif of Nef, known to be important for optimal viral replication, is part of a polyproline type II helix that engages the SH3 domain in a manner resembling closely the interaction of isolated peptides with SH3 domains. The Nef-SH3 structure also reveals how high affinity and specificity in the SH3 interaction is achieved by the presentation of the PxxP motif within the context of the folded structure of Nef.

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Related Citations: 

• 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
• A Single Amino Acid in the SH3 Domain of HCK Determines its High Affinity and Specificity in Binding to HIV-1 Nef Protein
  Lee, C.H.,Leung, B.,Lemmon, M.A.,Zheng, J.,Cowburn, D.,Kuriyan, J.,Saksela, K.
  (1995) Embo J. 14: 5006




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Organizational Affiliation: 

The Rockefeller University, New York, New York 10021, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
FYN TYROSINE KINASE	A, C	59	Homo sapiens	Mutation(s): 1  Gene Names: FYN EC: 2.7.10.2
Find proteins for P06241 (Homo sapiens) Go to Gene View: FYN Go to UniProtKB:  P06241

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 NEF PROTEIN	B, D	152	Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)	Mutation(s): 1  Gene Names: nef
Find proteins for P03406 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Go to UniProtKB:  P03406

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PBM	B, D	TRIMETHYL LEAD ION C3 H9 Pb SNBFOEGVGALPSE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.282 
• R-Value Work: 0.215 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 107.800	α = 90.00
b = 107.800	β = 90.00
c = 229.100	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
DENZO	data reduction
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-06-29 
• Released Date: 1997-01-11 
• Deposition Author(s): Lee, C.-H., Kuriyan, J.

Revision History 

• Version 1.0: 1997-01-11
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance