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 

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: 10.1016/j.str.2011.12.013

  • 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 subun ...

    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 asĀ 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 antiviralĀ 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-ASSOCIATED PROTEIN 1
A
118Homo sapiensMutation(s): 3 
Gene Names: UBAP1
Find proteins for Q9NZ09 (Homo sapiens)
Go to Gene View: UBAP1
Go to UniProtKB:  Q9NZ09
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
UBIQUITIN-ASSOCIATED PROTEIN 1
B
118Homo sapiensMutation(s): 3 
Gene Names: UBAP1
Find proteins for Q9NZ09 (Homo sapiens)
Go to Gene View: UBAP1
Go to UniProtKB:  Q9NZ09
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

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Download CCD File 
A, B
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
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 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 34.404α = 102.58
b = 43.480β = 96.47
c = 59.413γ = 113.24
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHENIXrefinement
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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