1EFN

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 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

  • DOI: 10.1016/s0092-8674(00)81276-3
  • Primary Citation of Related Structures:  
    1EFN

  • 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 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: 
    • 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 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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FYN TYROSINE KINASEA, C59Homo sapiensMutation(s): 1 
Gene Names: HIV-1 NEF, FYN
EC: 2.7.1.112 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06241 (Homo sapiens)
Explore P06241 
Go to UniProtKB:  P06241
PHAROS:  P06241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06241
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 NEF PROTEINB, D152Human immunodeficiency virus 1Mutation(s): 1 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03406
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PBM
Query on PBM
Download Ideal Coordinates CCD File 
E [auth B],
F [auth D]		TRIMETHYL LEAD ION
C3 H9 Pb
SNBFOEGVGALPSE-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.8α = 90
b = 107.8β = 90
c = 229.1γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-11
    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: 2021-11-03
    Changes: Database references, Derived calculations, Other