Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39193.41 
• Atom Count: 2704 
• Residue Count: 348 
• Unique protein chains: 1

2OJQ

Crystal structure of Alix V domain

• DOI: 10.2210/pdb2OJQ/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2007-01-13 Released: 2007-02-20 
• Deposition Author(s): Lee, S., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 0.318 
• R-Value Work: 0.250 

Literature

Structural basis for viral late-domain binding to Alix

Lee, S., Joshi, A., Nagashima, K., Freed, E.O., Hurley, J.H.

(2007) Nat.Struct.Mol.Biol. 14: 194-199

• PubMed: 17277784 
• DOI: 10.1038/nsmb1203


• PubMed Abstract: 
  

The modular protein Alix is a central node in endosomal-lysosomal trafficking and the budding of human immunodeficiency virus (HIV)-1. The Gag p6 protein of HIV-1 contains a LYPx(n)LxxL motif that is required for Alix-mediated budding and binds a region of Alix spanning residues 360-702. The structure of this fragment of Alix has the shape of the letter 'V' and is termed the V domain. The V domain has a topologically complex arrangement of 11 alpha-helices, with connecting loops that cross three times between the two arms of the V. The conserved residue Phe676 is at the center of a large hydrophobic pocket and is crucial for binding to a peptide model of HIV-1 p6. Overexpression of the V domain inhibits HIV-1 release from cells. This inhibition of release is reversed by mutations that block binding of the Alix V domain to p6.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), US Department of Health and Human Services, Bethesda, Maryland 20892, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death 6-interacting protein	A	348	Homo sapiens	Mutation(s): 0  Gene Names: PDCD6IP (AIP1, ALIX, KIAA1375)
Find proteins for Q8WUM4 (Homo sapiens) Go to Gene View: PDCD6IP Go to UniProtKB:  Q8WUM4

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 0.318 
• R-Value Work: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 37.650	α = 90.00
b = 55.380	β = 92.37
c = 113.166	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data collection
HKL-2000	data scaling
REFMAC	refinement
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-13 
• Released Date: 2007-02-20 
• Deposition Author(s): Lee, S., Hurley, J.H.

Revision History 

• Version 1.0: 2007-02-20
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.3: 2018-01-31
  Type: Experimental preparation