5UV6

Crystal structure of human Opioid Binding Protein/Cell Adhesion Molecule Like (OPCML)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65002 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.284 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions.

Birtley, J.R.Alomary, M.Zanini, E.Antony, J.Maben, Z.Weaver, G.C.Von Arx, C.Mura, M.Marinho, A.T.Lu, H.Morecroft, E.V.N.Karali, E.Chayen, N.E.Tate, E.W.Jurewicz, M.Stern, L.J.Recchi, C.Gabra, H.

(2019) Nat Commun 10: 3134-3134

  • DOI: 10.1038/s41467-019-10966-8

  • PubMed Abstract: 
  • OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impa ...

    OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal structure of this glycoprotein to 2.65 Å resolution. OPCML consists of an extended arrangement of three immunoglobulin-like domains and homodimerizes via a network of contacts between membrane-distal domains. We report the generation of a panel of OPCML variants with representative clinical mutations and demonstrate clear phenotypic effects in vitro and in vivo including changes to anchorage-independent growth, interaction with activated cognate receptor tyrosine kinases, cellular migration, invasion in vitro and tumor growth in vivo. Our results suggest that clinically occurring somatic missense mutations in OPCML have the potential to contribute to tumorigenesis in a variety of cancers.


    Organizational Affiliation

    Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK. c.recchi@imperial.ac.uk.,Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.,Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6HB, UK. h.gabra@imperial.ac.uk.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA. lawrence.stern@umassmed.edu.,UCB Pharma, Bath Road, Slough, SL1 3WE, UK.,Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK. h.gabra@imperial.ac.uk.,Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.,Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Opioid-binding protein/cell adhesion molecule
A, B
286Homo sapiensMutation(s): 0 
Gene Names: OPCML (IGLON1, OBCAM)
Membrane protein
mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Cell Adhesion Molecules
Protein: 
Opioid Binding Protein/Cell Adhesion Molecule Like (OPCML)
Find proteins for Q14982 (Homo sapiens)
Go to Gene View: OPCML
Go to UniProtKB:  Q14982
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65002 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.284 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.564α = 90.00
b = 93.564β = 90.00
c = 262.158γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
PHENIXrefinement
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesNIH-AI038996

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references
  • Version 1.2: 2019-12-11
    Type: Author supporting evidence