6S2M

Perdeuterated human myelin protein P2 at 0.72-A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.72 Å
  • R-Value Free: 0.111 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Sub-Atomic Resolution Crystal Structures Reveal Conserved Geometric Outliers at Functional Sites.

Laulumaa, S.Kursula, P.

(2019) Molecules 24

  • DOI: 10.3390/molecules24173044
  • Primary Citation of Related Structures:  
    6S2M, 6S2S

  • PubMed Abstract: 
  • Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0 ...

    Myelin protein 2 (P2) is a peripheral membrane protein of the vertebrate nervous system myelin sheath, having possible roles in both lipid transport and 3D molecular organization of the multilayered myelin membrane. We extended our earlier crystallographic studies on human P2 and refined its crystal structure at an ultrahigh resolution of 0.72 Å in perdeuterated form and 0.86 Å in hydrogenated form. Characteristic differences in C-H…O hydrogen bond patterns were observed between extended β strands, kinked or ending strands, and helices. Often, side-chain C-H groups engage in hydrogen bonding with backbone carbonyl moieties. The data highlight several amino acid residues with unconventional conformations, including both bent aromatic rings and twisted guanidinium groups on arginine side chains, as well as non-planar peptide bonds. In two locations, such non-ideal conformations cluster, providing proof of local functional strain. Other ultrahigh-resolution protein structures similarly contain chemical groups, which break planarity rules. For example, in Src homology 3 (SH3) domains, a conserved bent aromatic residue is observed near the ligand binding site. Fatty acid binding protein (FABP) 3, belonging to the same family as P2, has several side chains and peptide bonds bent exactly as those in P2. We provide a high-resolution snapshot on non-ideal conformations of amino acid residues under local strain, possibly relevant to biological function. Geometric outliers observed in ultrahigh-resolution protein structures are real and likely relevant for ligand binding and conformational changes. Furthermore, the deuteration of protein and/or solvent are promising variables in protein crystal optimization.


    Organizational Affiliation

    Department of Biomedicine, University of Bergen, 5020 Bergen, Norway. petri.kursula@uib.no.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myelin P2 proteinA133Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VCA (Subject of Investigation/LOI)
Query on VCA

Download Ideal Coordinates CCD File 
C [auth A]VACCENIC ACID
C18 H34 O2
UWHZIFQPPBDJPM-FPLPWBNLSA-N
 Ligand Interaction
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
B [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.72 Å
  • R-Value Free: 0.111 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.18α = 90
b = 36.21β = 97.03
c = 31.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sigrid Juselius FoundationFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references