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- PDB-2m8t: Solution NMR structure of the V209M variant of the human prion pr... -

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Basic information

Entry
Database: PDB / ID: 2m8t
TitleSolution NMR structure of the V209M variant of the human prion protein (residues 90-231)
ComponentsMajor prion protein
KeywordsCELL CYCLE / MEMBRANE PROTEIN
Function / homology
Function and homology information


: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport ...: / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of interleukin-2 production / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / negative regulation of amyloid-beta formation / cuprous ion binding / negative regulation of activated T cell proliferation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / negative regulation of type II interferon production / : / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / positive regulation of protein tyrosine kinase activity / response to cadmium ion / inclusion body / regulation of peptidyl-tyrosine phosphorylation / cellular response to copper ion / neuron projection maintenance / molecular condensate scaffold activity / tubulin binding / protein sequestering activity / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / postsynapse / nuclear membrane / response to oxidative stress / protease binding / transmembrane transporter binding / postsynaptic density / learning or memory / molecular adaptor activity / regulation of cell cycle / cell cycle / copper ion binding / membrane raft / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, MOLECULAR DYNAMICS
Model detailsfewest violations, model1
AuthorsMills, J.L. / Surewicz, K. / Surewicz, W. / Soennichsen, F.D.
CitationJournal: Cell Rep / Year: 2013
Title: Thermodynamic Stabilization of the Folded Domain of Prion Protein Inhibits Prion Infection in Vivo.
Authors: Kong, Q. / Mills, J.L. / Kundu, B. / Li, X. / Qing, L. / Surewicz, K. / Cali, I. / Huang, S. / Zheng, M. / Swietnicki, W. / Sonnichsen, F.D. / Gambetti, P. / Surewicz, W.K.
History
DepositionMay 28, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)16,5571
Polymers16,5571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 16557.396 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 90-231 / Mutation: V209M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIP, PRNP, PRP / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04156

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SOLUTION NMR STRUCTURE OF THE V209M VARIANT OF THE HUMAN PRION PROTEIN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-1H NOESY
1513D HNCA
1613D H(CCO)NH
1713D C(CO)NH
1813D (H)CCH
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11122D 1H-13C HSQC aliphatic
11213D HN(CA)CB
11313D CBCA(CO)NH
11413D HNCO
11513D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] MAJOR PRION PROTEIN, 10 mM sodium acetate, 0.005 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-5% 13C; U-99% 15N] MAJOR PRION PROTEIN, 10 mM sodium acetate, 0.005 w/v sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMAJOR PRION PROTEIN-1[U-99% 13C; U-99% 15N]1
10 mMsodium acetate-21
0.005 w/vsodium azide-31
1.0 mMMAJOR PRION PROTEIN-4[U-5% 13C; U-99% 15N]2
10 mMsodium acetate-52
0.005 w/vsodium azide-62
Sample conditionsIonic strength: 10 / pH: 4.6 / Pressure: AMBIENT atm / Temperature: 299 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
VARIAN INOVAVarianINOVA5001
BRUKER AVANCEBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003
Varian INOVAVarianINOVA9004

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
PROSAGuntertprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
MOLMOLKoradi, Billeter and Wuthrichdata analysis
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics, MOLECULAR DYNAMICS
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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