Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 79024.66 
• Atom Count: 5552 
• Residue Count: 705 
• Unique protein chains: 2

2R03

Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain

• DOI: 10.2210/pdb2R03/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, Equine infectious anemia virus (strain Wyoming)
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2007-08-17 Released: 2007-12-18 
• Deposition Author(s): Hill, C.P., Zhai, Q., Fisher, R.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.286 
• R-Value Work: 0.223 

Literature

Structural and functional studies of ALIX interactions with YPX(n)L late domains of HIV-1 and EIAV.

Zhai, Q., Fisher, R.D., Chung, H.Y., Myszka, D.G., Sundquist, W.I., Hill, C.P.

(2008) Nat.Struct.Mol.Biol. 15: 43-49

• PubMed: 18066081 
• DOI: 10.1038/nsmb1319
• Primary Citation of Related Structures:  
  2R05, 2R02


• PubMed Abstract: 
  

Retrovirus budding requires short peptide motifs (late domains) located within the viral Gag protein that function by recruiting cellular factors. The YPX(n)L late domains of HIV and other lentiviruses recruit the protein ALIX (also known as AIP1), which also functions in vesicle formation at the multivesicular body and in the abscission stage of cytokinesis. Here, we report the crystal structures of ALIX in complex with the YPX(n)L late domains from HIV-1 and EIAV. The two distinct late domains bind at the same site on the ALIX V domain but adopt different conformations that allow them to make equivalent contacts. Binding studies and functional assays verified the importance of key interface residues and revealed that binding affinities are tuned by context-dependent effects. These results reveal how YPX(n)L late domains recruit ALIX to facilitate virus budding and how ALIX can bind YPX(n)L sequences with both n = 1 and n = 3.

---

Organizational Affiliation: 

Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death 6-interacting protein	A	697	Homo sapiens	Mutation(s): 2  Gene Names: PDCD6IP (AIP1, ALIX, KIAA1375)
Find proteins for Q8WUM4 (Homo sapiens) Go to Gene View: PDCD6IP Go to UniProtKB:  Q8WUM4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
p6-Gag	B	8	Equine infectious anemia virus (strain Wyoming)	Mutation(s): 0  Gene Names: gag
Find proteins for P69732 (Equine infectious anemia virus (strain Wyoming)) Go to UniProtKB:  P69732

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.286 
• R-Value Work: 0.223 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 146.383	α = 90.00
b = 98.570	β = 107.07
c = 72.799	γ = 90.00

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data collection
HKL-2000	data reduction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-08-17 
• Released Date: 2007-12-18 
• Deposition Author(s): Hill, C.P., Zhai, Q., Fisher, R.D.

Revision History 

• Version 1.0: 2007-12-18
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-10-25
  Type: Refinement description