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- PDB-2kkg: NMR structure of the octarepeat region of prion protein bound to ... -

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Basic information

Entry
Database: PDB / ID: 2kkg
TitleNMR structure of the octarepeat region of prion protein bound to pentosan polysulfate
ComponentsMajor prion protein
KeywordsMEMBRANE PROTEIN / prion protein / octapeptide repeats / pentosan polysulfate / sulfated glycans / Cell membrane / Disulfide bond / Glycoprotein / Golgi apparatus / GPI-anchor / Lipoprotein / Membrane / Prion
Function / homology
Function and homology information


positive regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade ...positive regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / cuprous ion binding / 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 / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / terminal bouton / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / presynapse / signaling receptor activity / amyloid-beta binding / protease binding / microtubule binding / nuclear membrane / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / cell surface / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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 speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 2
AuthorsTaubner, L.M. / Caughey, B. / Copie, V.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan.
Authors: Taubner, L.M. / Bienkiewicz, E.A. / Copie, V. / Caughey, B.
History
DepositionJun 19, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)8,6961
Polymers8,6961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1

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Components

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


Mass: 8696.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / References: UniProt: P04273

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: residues 57-91 of Syrian hamster prion protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D H(CCO)NH
1933D (H)CCH-TOCSY
11013D 1H-15N NOESY
11133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-15N] octarepeats-1, 5 % [U-2H] D2O-2, 20 % [U-2H] DMSO-3, 20 mM pentosan polysulfate-4, 10 mM sodium acetate-5, 75 % H2O-6, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-13C; U-15N] octarepeats-13, 80 % [U-2H] D2O-14, 20 % [U-2H] DMSO-15, 20 mM pentosan polysulfate-16, 10 mM sodium acetate-17, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMoctarepeats-1[U-15N]1
5 %D2O-2[U-2H]1
20 %DMSO-3[U-2H]1
20 mMpentosan polysulfate-41
10 mMsodium acetate-51
75 %H2O-61
0.5 mMoctarepeats-7[U-13C; U-15N]2
5 %D2O-8[U-2H]2
20 %DMSO-9[U-2H]2
20 mMpentosan polysulfate-102
10 mMsodium acetate-112
75 %H2O-122
0.5 mMoctarepeats-13[U-13C; U-15N]3
80 %D2O-14[U-2H]3
20 %DMSO-15[U-2H]3
20 mMpentosan polysulfate-163
10 mMsodium acetate-173
Sample conditionspH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ProcheckNMRLaskowski and MacArthurgeometry optimization
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 285 / NOE intraresidue total count: 81 / NOE medium range total count: 59 / NOE sequential total count: 145
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.2 Å
NMR ensemble rmsDistance rms dev: 0.99 Å

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