4D6A

Human myelin protein P2 after neutron scattering experiments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynamics of the Peripheral Membrane Protein P2 from Human Myelin Measured by Neutron Scattering-A Comparison between Wild-Type Protein and a Hinge Mutant.

Laulumaa, S.Nieminen, T.Lehtimaki, M.Aggarwal, S.Simons, M.Koza, M.M.Vattulainen, I.Kursula, P.Natali, F.

(2015) Plos One 10: 28954

  • DOI: 10.1371/journal.pone.0128954
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Myelin protein P2 is a fatty acid-binding structural component of the myelin sheath in the peripheral nervous system, and its function is related to its membrane binding capacity. Here, the link between P2 protein dynamics and structure and function ...

    Myelin protein P2 is a fatty acid-binding structural component of the myelin sheath in the peripheral nervous system, and its function is related to its membrane binding capacity. Here, the link between P2 protein dynamics and structure and function was studied using elastic incoherent neutron scattering (EINS). The P38G mutation, at the hinge between the β barrel and the α-helical lid, increased the lipid stacking capacity of human P2 in vitro, and the mutated protein was also functional in cultured cells. The P38G mutation did not change the overall structure of the protein. For a deeper insight into P2 structure-function relationships, information on protein dynamics in the 10 ps to 1 ns time scale was obtained using EINS. Values of mean square displacements mainly from protein H atoms were extracted for wild-type P2 and the P38G mutant and compared. Our results show that at physiological temperatures, the P38G mutant is more dynamic than the wild-type P2 protein, especially on a slow 1-ns time scale. Molecular dynamics simulations confirmed the enhanced dynamics of the mutant variant, especially within the portal region in the presence of bound fatty acid. The increased softness of the hinge mutant of human myelin P2 protein is likely related to an enhanced flexibility of the portal region of this fatty acid-binding protein, as well as to its interactions with the lipid bilayer surface requiring conformational adaptations.


    Organizational Affiliation

    Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland; German Electron Synchrotron (DESY), Hamburg, Germany; European Spallation Source (ESS), Lund, Sweden.




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 2 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
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.147 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.670α = 90.00
b = 57.670β = 90.00
c = 100.660γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection