4AE4

The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a novel SOUBA domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain.

Agromayor, M.Soler, N.Caballe, A.Kueck, T.Freund, S.M.Allen, M.D.Bycroft, M.Perisic, O.Ye, Y.McDonald, B.Scheel, H.Hofmann, K.Neil, S.J.Martin-Serrano, J.Williams, R.L.

(2012) Structure 20: 414-428

  • DOI: https://doi.org/10.1016/j.str.2011.12.013
  • Primary Citation of Related Structures:  
    4AE4

  • PubMed Abstract: 

    The endosomal sorting complexes required for transport (ESCRTs) facilitate endosomal sorting of ubiquitinated cargo, MVB biogenesis, late stages of cytokinesis, and retroviral budding. Here we show that ubiquitin associated protein 1 (UBAP1), a subunit of human ESCRT-I, coassembles in a stable 1:1:1:1 complex with Vps23/TSG101, VPS28, and VPS37. The X-ray crystal structure of the C-terminal region of UBAP1 reveals a domain that we describe as a solenoid of overlapping UBAs (SOUBA). NMR analysis shows that each of the three rigidly arranged overlapping UBAs making up the SOUBA interact with ubiquitin. We demonstrate that UBAP1-containing ESCRT-I is essential for degradation of antiviral cell-surface proteins, such as tetherin (BST-2/CD317), by viral countermeasures, namely, the HIV-1 accessory protein Vpu and the Kaposi sarcoma-associated herpesvirus (KSHV) ubiquitin ligase K5.


  • Organizational Affiliation

    Department of Infectious Diseases, King's College London School of Medicine, London SE1 9RT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-ASSOCIATED PROTEIN 1118Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ09 (Homo sapiens)
Explore Q9NZ09 
Go to UniProtKB:  Q9NZ09
PHAROS:  Q9NZ09
GTEx:  ENSG00000165006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ09
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBIQUITIN-ASSOCIATED PROTEIN 1118Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ09 (Homo sapiens)
Explore Q9NZ09 
Go to UniProtKB:  Q9NZ09
PHAROS:  Q9NZ09
GTEx:  ENSG00000165006 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ09
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NHE
Query on NHE

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
MSO
Query on MSO
B
L-PEPTIDE LINKINGC5 H11 N O3 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.404α = 102.58
b = 43.48β = 96.47
c = 59.413γ = 113.24
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references