5LM1

Crystal Structure of HD-PTP phosphatase in complex with UBAP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1.

Gahloth, D.Levy, C.Heaven, G.Stefani, F.Wunderley, L.Mould, P.Cliff, M.J.Bella, J.Fielding, A.J.Woodman, P.Tabernero, L.

(2016) Structure 24: 2115-2126

  • DOI: https://doi.org/10.1016/j.str.2016.10.006
  • Primary Citation of Related Structures:  
    5LM1, 5LM2

  • PubMed Abstract: 

    Endosomal sorting complexes required for transport (ESCRTs) are essential for ubiquitin-dependent degradation of mitogenic receptors, a process often compromised in cancer pathologies. Sorting of ubiquinated receptors via ESCRTs is controlled by the tumor suppressor phosphatase HD-PTP. The specific interaction between HD-PTP and the ESCRT-I subunit UBAP1 is critical for degradation of growth factor receptors and integrins. Here, we present the structural characterization by X-ray crystallography and double electron-electron resonance spectroscopy of the coiled-coil domain of HD-PTP and its complex with UBAP1. The coiled-coil domain adopts an unexpected open and rigid conformation that contrasts with the closed and flexible coiled-coil domain of the related ESCRT regulator Alix. The HD-PTP:UBAP1 structure identifies the molecular determinants of the interaction and provides a molecular basis for the specific functional cooperation between HD-PTP and UBAP1. Our findings provide insights into the molecular mechanisms of regulation of ESCRT pathways that could be relevant to anticancer therapies.


  • Organizational Affiliation

    School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 23352Homo sapiensMutation(s): 0 
Gene Names: PTPN23KIAA1471
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3S7 (Homo sapiens)
Explore Q9H3S7 
Go to UniProtKB:  Q9H3S7
PHAROS:  Q9H3S7
GTEx:  ENSG00000076201 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3S7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
UBAP-120Homo sapiensMutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.93α = 90
b = 93.27β = 90
c = 102.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2016-11-30 
  • Deposition Author(s): Levy, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references