8VM1 | pdb_00008vm1

Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction

  • Classification: CELL ADHESION
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-01-12 Released: 2024-09-04 
  • Deposition Author(s): Rupert, P.B., Strong, R.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.298 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural elucidation of the mesothelin-mucin-16/CA125 interaction.

Rupert, P.B.Buerger, M.Friend, D.J.Strong, R.K.

(2024) Structure 32: 1049-1054.e2

  • DOI: https://doi.org/10.1016/j.str.2024.04.011
  • Primary Citation Related Structures: 
    8VM1

  • PubMed Abstract: 

    Mesothelin (MSLN) is a cell-surface glycoprotein expressed at low levels on normal mesothelium but overexpressed in many cancers. Mesothelin has been implicated to play role/s in cell adhesion and multiple signaling pathways. Mucin-16/CA125 is an enormous cell-surface glycoprotein, also normally expressed on mesothelium and implicated in the progression and metastasis of several cancers, and directly binds mesothelin. However, the precise biological function/s of mesothelin and mucin-16/CA125 remain mysterious. We report protein engineering and recombinant production, qualitative and quantitative binding studies, and a crystal structure determination elucidating the molecular-level details governing recognition of mesothelin by mucin-16/CA125. The interface is small, consistent with the ∼micromolar binding constant and is free of glycan-mediated interactions. Sequence comparisons and modeling suggest that multiple mucin-16/CA125 modules can interact with mesothelin through comparable interactions, potentially generating a high degree of avidity at the cell surface to overcome the weak affinity, with implications for functioning and therapeutic interventions.


  • Organizational Affiliation
    • Division of Basic Science, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 22.91 kDa 
  • Atom Count: 1,544 
  • Modeled Residue Count: 185 
  • Deposited Residue Count: 192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mesothelin, cleaved form,Mucin-16192Homo sapiensMutation(s): 0 
Gene Names: MSLNMPFMUC16CA125
UniProt & NIH Common Fund Data Resources
Find proteins for Q13421 (Homo sapiens)
Explore Q13421 
Go to UniProtKB:  Q13421
PHAROS:  Q13421
GTEx:  ENSG00000102854 
Find proteins for Q8WXI7 (Homo sapiens)
Explore Q8WXI7 
Go to UniProtKB:  Q8WXI7
PHAROS:  Q8WXI7
GTEx:  ENSG00000181143 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ13421Q8WXI7
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q13421-1Q8WXI7-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]3N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO
GlyCosmos: G62182OO
GlyGen: G62182OO

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.298 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.203α = 90
b = 73.237β = 90
c = 75.054γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01A|176563
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA015704

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary