1YIV | pdb_00001yiv

Structure of myelin P2 protein from Equine spinal cord

• PDB DOI: https://doi.org/10.2210/pdb1YIV/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2005-01-13 Released: 2005-07-26 
• Deposition Author(s): Hunter, D.J.B., MacMaster, R., Rozak, A.W., Riboldi-Tunnicliffe, A., Grifiths, I.R., Freer, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structure of myelin P2 protein from equine spinal cord.

Hunter, D.J., Macmaster, R., Roszak, A.W., Riboldi-Tunnicliffe, A., Griffiths, I.R., Freer, A.A.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1067-1071

• PubMed: 16041071 
• DOI: https://doi.org/10.1107/S0907444905014162
• Primary Citation Related Structures: 
  1YIV


• PubMed Abstract: 
  

  Equine P2 protein has been isolated from horse spinal cord and its structure determined to 2.1 A. Since equine myelin is a viable alternative to bovine tissue for large-scale preparations, characterization of the proteins from equine spinal cord myelin has been initiated. There is an unusually high amount of P2 protein in equine CNS myelin compared with other species. The structure was determined by molecular replacement and subsequently refined to an R value of 0.187 (Rfree=0.233). The structure contains a molecule of the detergent LDAO and HEPES buffer in the binding cavity and is otherwise analogous to other cellular retinol-binding proteins.

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Organizational Affiliation: 
• Department of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, Scotland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.95 kDa 
• Atom Count: 1,150 
• Modeled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myelin P2 protein	A	131	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P0C6G6 (Equus caballus) Explore P0C6G6  Go to UniProtKB:  P0C6G6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
LDA	C [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.846	α = 90
b = 45.846	β = 90
c = 125.778	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Hunter, D.J.B., MacMaster, R., Rozak, A.W., Riboldi-Tunnicliffe, A., Grifiths, I.R., Freer, A.A.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description