7O60

Crystal structure of human myelin protein P2 at room temperature from joint X-ray and neutron refinement.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.160 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.299 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Human myelin protein P2: from crystallography to time-lapse membrane imaging and neuropathy-associated variants.

Uusitalo, M.Klenow, M.B.Laulumaa, S.Blakeley, M.P.Simonsen, A.C.Ruskamo, S.Kursula, P.

(2021) FEBS J 288: 6716-6735

  • DOI: https://doi.org/10.1111/febs.16079
  • Primary Citation of Related Structures:  
    7NRW, 7NSR, 7NTP, 7O60

  • PubMed Abstract: 

    Peripheral myelin protein 2 (P2) is a fatty acid-binding protein expressed in vertebrate peripheral nervous system myelin, as well as in human astrocytes. Suggested functions of P2 include membrane stacking and lipid transport. Mutations in the PMP2 gene, encoding P2, are associated with Charcot-Marie-Tooth disease (CMT). Recent studies have revealed three novel PMP2 mutations in CMT patients. To shed light on the structure and function of these P2 variants, we used X-ray and neutron crystallography, small-angle X-ray scattering, circular dichroism spectroscopy, computer simulations and lipid binding assays. The crystal and solution structures of the I50del, M114T and V115A variants of P2 showed minor differences to the wild-type protein, whereas their thermal stability was reduced. Vesicle aggregation assays revealed no change in membrane stacking characteristics, while the variants showed altered fatty acid binding. Time-lapse imaging of lipid bilayers indicated formation of double-membrane structures induced by P2, which could be related to its function in stacking of two myelin membrane surfaces in vivo. In order to better understand the links between structure, dynamics and function, the crystal structure of perdeuterated P2 was refined from room temperature data using neutrons and X-rays, and the results were compared to simulations and cryocooled crystal structures. Our data indicate similar properties for all known human P2 CMT variants; while crystal structures are nearly identical, thermal stability and function of CMT variants are impaired. Our data provide new insights into the structure-function relationships and dynamics of P2 in health and disease.


  • Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myelin P2 protein133Homo sapiensMutation(s): 0 
Gene Names: PMP2
UniProt & NIH Common Fund Data Resources
Find proteins for P02689 (Homo sapiens)
Explore P02689 
Go to UniProtKB:  P02689
PHAROS:  P02689
GTEx:  ENSG00000147588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02689
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
C [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.160 
  • Space Group: P 41 21 2
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.341 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.299 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.952α = 90
b = 57.952β = 90
c = 100.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Structure summary
  • Version 1.2: 2021-12-15
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary