2WUT

Crystal structure of human myelin protein P2 in complex with palmitate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural and Functional Characterization of Human Peripheral Nervous System Myelin Protein P2.

Majava, V.Polverini, E.Mazzini, A.Nanekar, R.Knoll, W.Peters, J.Natali, F.Baumgartel, P.Kursula, I.Kursula, P.

(2010) PLoS One 5: E300

  • DOI: https://doi.org/10.1371/journal.pone.0010300
  • Primary Citation of Related Structures:  
    2WUT

  • PubMed Abstract: 

    The myelin sheath is a tightly packed multilayered membrane structure insulating selected axons in the central and the peripheral nervous systems. Myelin is a biochemically unique membrane, containing a specific set of proteins. In this study, we expressed and purified recombinant human myelin P2 protein and determined its crystal structure to a resolution of 1.85 A. A fatty acid molecule, modeled as palmitate based on the electron density, was bound inside the barrel-shaped protein. Solution studies using synchrotron radiation indicate that the crystal structure is similar to the structure of the protein in solution. Docking experiments using the high-resolution crystal structure identified cholesterol, one of the most abundant lipids in myelin, as a possible ligand for P2, a hypothesis that was proven by fluorescence spectroscopy. In addition, electrostatic potential surface calculations supported a structural role for P2 inside the myelin membrane. The potential membrane-binding properties of P2 and a peptide derived from its N terminus were studied. Our results provide an enhanced view into the structure and function of the P2 protein from human myelin, which is able to bind both monomeric lipids inside its cavity and membrane surfaces.


  • Organizational Affiliation

    Department of Biochemistry, University of Oulu, Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MYELIN P2 PROTEIN133Homo sapiensMutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.33α = 90
b = 66.33β = 90
c = 101.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description