4U5W | pdb_00004u5w

Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains

• PDB DOI: https://doi.org/10.2210/pdb4U5W/pdb

• Classification: Viral protein/Transferase
• Organism(s): HIV-1 M:B_ARV2/SF2, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-25 Released: 2014-08-20 
• Deposition Author(s): Alvarado, J.J., Yeh, J.I., Smithgall, T.E.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Models: experimental

Literature

Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment.

Alvarado, J.J., Tarafdar, S., Yeh, J.I., Smithgall, T.E.

(2014) J Biological Chem 289: 28539-28553

• PubMed: 25122770 
• DOI: https://doi.org/10.1074/jbc.M114.600031
• Primary Citation Related Structures: 
  4U5W


• PubMed Abstract: 
  

  HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners.

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Organizational Affiliation: 
• From the Departments of Microbiology and Molecular Genetics and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and.
From the Departments of Microbiology and Molecular Genetics and Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.
Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and [e-mail].
From the Departments of Microbiology and Molecular Genetics and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.79 kDa 
• Atom Count: 5,067 
• Modeled Residue Count: 550 
• Deposited Residue Count: 658 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Nef	A, C	149	HIV-1 M:B_ARV2/SF2	Mutation(s): 0  Gene Names: nef
UniProt
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03407  Go to UniProtKB:  P03407

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase HCK	B, D	180	Homo sapiens	Mutation(s): 0  Gene Names: HCK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P08631 (Homo sapiens) Explore P08631  Go to UniProtKB:  P08631
PHAROS:  P08631 GTEx:  ENSG00000101336

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
MPD	E [auth A], F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.195 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.489	α = 112.28
b = 57.265	β = 96.09
c = 72.111	γ = 106

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Alvarado, J.J., Yeh, J.I., Smithgall, T.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI057083
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI102724
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082251

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2014-08-27
  Changes: Database references
• Version 1.2: 2014-10-22
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description