4BVM

The peripheral membrane protein P2 from human myelin at atomic resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Atomic Resolution View Into the Structure-Function Relationships of the Human Myelin Peripheral Membrane Protein P2

Ruskamo, S.Yadav, R.P.Sharma, S.Lehtimaki, M.Laulumaa, S.Aggarwal, S.Simons, M.Burck, J.Ulrich, A.S.Juffer, A.H.Kursula, I.Kursula, P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 165

  • DOI: https://doi.org/10.1107/S1399004713027910
  • Primary Citation of Related Structures:  
    4BVM

  • PubMed Abstract: 

    P2 is a fatty acid-binding protein expressed in vertebrate peripheral nerve myelin, where it may function in bilayer stacking and lipid transport. P2 binds to phospholipid membranes through its positively charged surface and a hydrophobic tip, and accommodates fatty acids inside its barrel structure. The structure of human P2 refined at the ultrahigh resolution of 0.93 Å allows detailed structural analyses, including the full organization of an internal hydrogen-bonding network. The orientation of the bound fatty-acid carboxyl group is linked to the protonation states of two coordinating arginine residues. An anion-binding site in the portal region is suggested to be relevant for membrane interactions and conformational changes. When bound to membrane multilayers, P2 has a preferred orientation and is stabilized, and the repeat distance indicates a single layer of P2 between membranes. Simulations show the formation of a double bilayer in the presence of P2, and in cultured cells wild-type P2 induces membrane-domain formation. Here, the most accurate structural and functional view to date on P2, a major component of peripheral nerve myelin, is presented, showing how it can interact with two membranes simultaneously while going through conformational changes at its portal region enabling ligand transfer.


  • 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: 0.93 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.07α = 90
b = 58.07β = 90
c = 101.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata 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: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 2.0: 2018-01-17
    Changes: Atomic model, Data collection
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description