2XS8

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

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 

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This is version 1.2 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROGRAMMED CELL DEATH 6-INTERACTING PROTEINA704Homo sapiensMutation(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
GTEx:  ENSG00000170248 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUM4
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SIVAGMTAN-1 GAG P6B18Simian immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for Q02843 (Simian immunodeficiency virus agm.grivet (isolate AGM gr-1))
Explore Q02843 
Go to UniProtKB:  Q02843
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02843
Protein Feature View
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  • Reference Sequence
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 = 145.542α = 90
b = 99.076β = 106.87
c = 72.594γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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