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- PDB-2lh8: Syrian hamster prion protein with thiamine -

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Basic information

Entry
Database: PDB / ID: 2lh8
TitleSyrian hamster prion protein with thiamine
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / prion / thiamine
Function / homology
Function and homology information


regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / : / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily ...Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-VIB / Major prion protein
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsPerez-Pineiro, R. / Bjorndahl, T.C. / Berjanskii, M. / Hau, D. / Li, L. / Huang, A. / Lee, R. / Gibbs, E. / Ladner, C. / Wei Dong, Y. ...Perez-Pineiro, R. / Bjorndahl, T.C. / Berjanskii, M. / Hau, D. / Li, L. / Huang, A. / Lee, R. / Gibbs, E. / Ladner, C. / Wei Dong, Y. / Abera, A. / Cashman, N.R. / Wishart, D.
CitationJournal: Febs J. / Year: 2011
Title: The prion protein binds thiamine.
Authors: Perez-Pineiro, R. / Bjorndahl, T.C. / Berjanskii, M.V. / Hau, D. / Li, L. / Huang, A. / Lee, R. / Gibbs, E. / Ladner, C. / Dong, Y.W. / Abera, A. / Cashman, N.R. / Wishart, D.S.
History
DepositionAug 5, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7232
Polymers12,4581
Non-polymers2651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 12457.793 Da / Num. of mol.: 1 / Fragment: UNP residues 125-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / Strain (production host): B12(DE3) / References: UniProt: P04273
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N4OS / Comment: medication*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution NMR structure of the core syrian hamster prion protein with thiamine
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1421D STD-TOCSY
1532D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 15N] shPrP, 10 mM thiamine, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM shPrP, 12.5 mM thiamine, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM shPrP, 10 mM thiamine, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMshPrP-1[U-100% 15N]1
10 mMthiamine-21
0.5 mMshPrP-32
12.5 mMthiamine-42
0.5 mMshPrP-53
10 mMthiamine-63
Sample conditionsIonic strength: 0.02 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRDraw3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1 / Conformers submitted total number: 1 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å

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