Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 80.83 kDa 
• Atom Count: 5,581 
• Modelled Residue Count: 706 
• Deposited Residue Count: 722 
• Unique protein chains: 2

 2XS8

Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain

• PDB DOI:  https://doi.org/10.2210/pdb2XS8/pdb

• Classification: PROTEIN TRANSPORT/VIRAL PROTEIN
• Organism(s): Homo sapiens, Simian immunodeficiency virus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2010-09-24 Released: 2010-11-03 
• Deposition Author(s): Zhai, Q., Landesman, M., Robinson, H., Sundquist, W.I., Hill, C.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Literature

Identification and Structural Characterization of the Alix-Binding Late Domains of Sivmac239 and Sivagmtan-1.

Zhai, Q., Landesman, M., Robinson, H., Sundquist, W.I., Hill, C.P.

(2011) J Virol 85: 632

• PubMed: 20962096 
• DOI: https://doi.org/10.1128/JVI.01683-10
• Primary Citation of Related Structures:  
  2XS1, 2XS8


• PubMed Abstract: 
  

Retroviral Gag proteins contain short late-domain motifs that recruit cellular ESCRT pathway proteins to facilitate virus budding. ALIX-binding late domains often contain the core consensus sequence YPX(n)L (where X(n) can vary in sequence and length). However, some simian immunodeficiency virus (SIV) Gag proteins lack this consensus sequence, yet still bind ALIX. We mapped divergent, ALIX-binding late domains within the p6(Gag) proteins of SIV(mac239) ((40)SREKPYKEVTEDLLHLNSLF(59)) and SIV(agmTan-1) ((24)AAGAYDPARKLLEQYAKK(41)). Crystal structures revealed that anchoring tyrosines (in lightface) and nearby hydrophobic residues (underlined) contact the ALIX V domain, revealing how lentiviruses employ a diverse family of late-domain sequences to bind ALIX and promote virus budding.

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Organizational Affiliation: 

Department of Biochemistry, University of Utah School of Medicine, 15 N. Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROGRAMMED CELL DEATH 6-INTERACTING PROTEIN	A	704	Homo sapiens	Mutation(s): 2  Gene Names: PDCD6IP, AIP1, ALIX, KIAA1375
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUM4 (Homo sapiens) Explore Q8WUM4  Go to UniProtKB:  Q8WUM4
PHAROS:  Q8WUM4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SIVAGMTAN-1 GAG P6	B	18	Simian immunodeficiency virus	Mutation(s): 0
UniProt
Find proteins for Q02843 (Simian immunodeficiency virus agm.grivet (isolate AGM gr-1)) Explore Q02843  Go to UniProtKB:  Q02843

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.542	α = 90
b = 99.076	β = 106.87
c = 72.594	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-03 
Deposition Author(s): Zhai, Q., Landesman, M., Robinson, H., Sundquist, W.I., Hill, C.P.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance