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 

wwPDB Validation 3D Report Full Report


This is version 2.0 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.,Sect.D 70: 165

  • DOI: 10.1107/S1399004713027910

  • 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 ac ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYELIN P2 PROTEIN
A
133Homo sapiensMutation(s): 0 
Gene Names: PMP2
Find proteins for P02689 (Homo sapiens)
Go to Gene View: PMP2
Go to UniProtKB:  P02689
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
VCA
Query on VCA

Download SDF File 
Download CCD File 
A
VACCENIC ACID
(11E)-OCTADEC-11-ENOIC ACID
C18 H34 O2
UWHZIFQPPBDJPM-FPLPWBNLSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.104 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.070α = 90.00
b = 58.070β = 90.00
c = 101.500γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-01-22
    Type: Database references
  • Version 2.0: 2018-01-17
    Type: Atomic model, Data collection