3TB8 | pdb_00003tb8

Crystal structure of full-length myristoylated HIV-1 Nef

• PDB DOI: https://doi.org/10.2210/pdb3TB8/pdb

• Classification: APOPTOSIS
• Organism(s): Human immunodeficiency virus type 1 BH10
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-08-05 Released: 2012-10-03 
• Deposition Author(s): Dennis, C.A., Harris, M., Jaeger, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free: 
  0.337 (Depositor), 0.430 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.440 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal structure of full-length myristoylated HIV-1 Nef

Dennis, C.A., Harris, M., Jaeger, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.46 kDa 
• Atom Count: 203 
• Modeled Residue Count: 203 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Nef	A	206	Human immunodeficiency virus type 1 BH10	Mutation(s): 1  Gene Names: nef
UniProt
Find proteins for P03404 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03404  Go to UniProtKB:  P03404

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.71 Å
• R-Value Free:  0.337 (Depositor), 0.430 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.440 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.33	α = 90
b = 89.33	β = 90
c = 27.78	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Dennis, C.A., Harris, M., Jaeger, J.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references
• Version 1.2: 2024-05-22
  Changes: Data collection