1EFN

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 seque ...

    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.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FYN TYROSINE KINASE
A, C
59Homo sapiensGene 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
MoleculeChainsSequence LengthOrganismDetails
HIV-1 NEF PROTEIN
B, D
152Human immunodeficiency virus type 1 group M subtype BGene Names: nef
Find proteins for P03406 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03406
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBM
Query on PBM

Download SDF File 
Download CCD File 
B, D
TRIMETHYL LEAD ION
C3 H9 Pb
SNBFOEGVGALPSE-UHFFFAOYSA-N
 Ligand Interaction
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 = 107.800α = 90.00
b = 107.800β = 90.00
c = 229.100γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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