8IIA

Crystal structure of the oligomeric state of the extracellular domain of human myelin protein zero(MPZ/P0)

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

  • Deposited: 2023-02-24 Released: 2023-08-30 
  • Deposition Author(s): Sakakura, M., Tanabe, M., Mio, K.
  • Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural bases for the Charcot-Marie-Tooth disease induced by single amino acid substitutions of myelin protein zero.

Sakakura, M.Tanabe, M.Mori, M.Takahashi, H.Mio, K.

(2023) Structure 31: 1452

  • DOI: https://doi.org/10.1016/j.str.2023.08.016
  • Primary Citation of Related Structures:  
    8IIA

  • PubMed Abstract: 

    Myelin protein zero (MPZ or P0) is a transmembrane protein which functions to glue membranes in peripheral myelin. Inter-membrane adhesion is mediated by homophilic interactions between the extracellular domains (ECDs) of MPZ. Single amino acid substitutions in an ECD cause demyelinating neuropathy, Charcot-Marie-Tooth disease (CMT), with unknown mechanisms. In this study, by using a novel assay system "nanomyelin," we revealed that a stacked-rings-like ECD-8-mer is responsible for membrane adhesion. Two inter-ECD interactions, cis and head-to-head, are essential to constituting the 8-mer and to gluing the membranes. This result was reinforced by the observation that the CMT-related N87H substitution at the cis interface abolished membrane-adhesion activity. In contrast, the CMT-related D32G and E68V variants retained membrane-stacking activity, whereas their thermal stability was lower than that of the WT. Reduced thermal stability may lead to impairment of the long-term stability of ECD and the layered membranes of myelin.


  • Organizational Affiliation

    Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan. Electronic address: sakakura@yokohama-cu.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myelin protein P0123Homo sapiensMutation(s): 0 
Gene Names: MPZ
UniProt & NIH Common Fund Data Resources
Find proteins for P25189 (Homo sapiens)
Explore P25189 
Go to UniProtKB:  P25189
PHAROS:  P25189
GTEx:  ENSG00000158887 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25189
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.579α = 90
b = 88.579β = 90
c = 88.988γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21K06515
Japan Society for the Promotion of Science (JSPS)Japan18K06601
Japan Science and TechnologyJapanJP18071859
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101070
Japan Agency for Medical Research and Development (AMED)JapanJP22ama1210001j001

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Database references
  • Version 1.2: 2023-11-15
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Structure summary