1EFN

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

• PDB DOI: https://doi.org/10.2210/pdb1EFN/pdb

• Classification: COMPLEX (SH3 DOMAIN/VIRAL ENHANCER)
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• 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: 2.50 Å
• R-Value Free: 0.282 
• R-Value Work: 0.215 
• R-Value Observed: 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 
• DOI: https://doi.org/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 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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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.43 kDa 
• Atom Count: 2,742 
• Modelled Residue Count: 322 
• Deposited Residue Count: 422 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FYN TYROSINE KINASE	A, C	59	Homo sapiens	Mutation(s): 1  Gene Names: HIV-1 NEF 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 GTEx:  ENSG00000010810

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 NEF PROTEIN	B, D	152	Human immunodeficiency virus 1	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PBM	E [auth B], F [auth D]	TRIMETHYL LEAD ION C3 H9 Pb SNBFOEGVGALPSE-UHFFFAOYSA-N

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 = 107.8	α = 90
b = 107.8	β = 90
c = 229.1	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.4: 2024-02-07
  Changes: Data collection