2R05

Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1038/nsmb1319
  • Primary Citation of Related Structures:  
    2R05, 2R03, 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), w ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Programmed cell death 6-interacting proteinA697Homo sapiensMutation(s): 2 
Gene Names: PDCD6IPAIP1ALIXKIAA1375
Find proteins for Q8WUM4 (Homo sapiens)
Explore Q8WUM4 
Go to UniProtKB:  Q8WUM4
NIH Common Fund Data Resources
PHAROS  Q8WUM4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
p6-GagB11N/AMutation(s): 0 
Find proteins for P35962 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2))
Explore P35962 
Go to UniProtKB:  P35962
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.09α = 90
b = 99.44β = 107.29
c = 73.543γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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