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  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
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 
• Modelled Residue Count: 550 
• Deposited Residue Count: 658 
• Unique protein chains: 2

 4U5W

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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.195 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

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 Biol Chem 289: 28539-28553

• PubMed: 25122770 
• DOI: https://doi.org/10.1074/jbc.M114.600031
• Primary Citation of 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.

---

Organizational Affiliation: 

From the Departments of Microbiology and Molecular Genetics and [e-mail].

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

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 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• 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.

---

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