4ORZ

HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain

• PDB DOI: https://doi.org/10.2210/pdb4ORZ/pdb

• Classification: TRANSFERASE/APOPTOSIS/IMMUNE SYSTEM
• Organism(s): Homo sapiens, HIV-1 M:B_ARV2/SF2, Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-12 Released: 2014-03-26 
• Deposition Author(s): Geyer, M., Lulf, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Structural basis for the inhibition of HIV-1 Nef by a high-affinity binding single-domain antibody.

Lulf, S., Matz, J., Rouyez, M.C., Jarviluoma, A., Saksela, K., Benichou, S., Geyer, M.

(2014) Retrovirology 11: 24-24

• PubMed: 24620746 
• DOI: https://doi.org/10.1186/1742-4690-11-24
• Primary Citation of Related Structures:  
  4ORZ


• PubMed Abstract: 
  

  The HIV-1 Nef protein is essential for AIDS pathogenesis by its interaction with host cell surface receptors and signaling factors. Despite its critical role as a virulence factor Nef is not targeted by current antiviral strategies.

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Organizational Affiliation: 

Center of Advanced European Studies and Research, Group Physical Biochemistry, Bonn, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.44 kDa 
• Atom Count: 2,455 
• Modelled Residue Count: 287 
• Deposited Residue Count: 332 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase HCK	A	67	Homo sapiens	Mutation(s): 6  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Nef	B	145	HIV-1 M:B_ARV2/SF2	Mutation(s): 4  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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
single domain antibody sdAb19	C	120	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73	α = 90
b = 73	β = 90
c = 71	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-26 
Deposition Author(s): Geyer, M., Lulf, S.

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description