5UV6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 

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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1038/s41467-019-10966-8
  • Primary Citation of Related Structures:  
    5UV6

  • 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 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

    Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Opioid-binding protein/cell adhesion molecule
A, B
286Homo sapiensMutation(s): 0 
Gene Names: OPCMLIGLON1OBCAM
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14982 (Homo sapiens)
Explore Q14982 
Go to UniProtKB:  Q14982
PHAROS:  Q14982
GTEx:  ENSG00000183715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14982
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q14982-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.285 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.564α = 90
b = 93.564β = 90
c = 262.158γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Database references, Refinement description, Structure summary