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- PDB-1b10: SOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1b10
TitleSOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEIN RPRP(90-231) , 25 STRUCTURES
ComponentsPROTEIN (PRION PROTEIN)
KeywordsPRION PROTEIN / PRION / SCRAPIE / BRAIN / GLYCOPROTEIN
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
Biological speciesMesocricetus auratus (golden hamster)
MethodSOLUTION NMR / NMR-RESTRAINED SIMULATED ANNEALING, MOLECULAR DYNAMICS, AND ENERGY MINIMIZATION.
AuthorsJames, T.L. / Liu, H. / Ulyanov, N.B. / Farr-Jones, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform.
Authors: James, T.L. / Liu, H. / Ulyanov, N.B. / Farr-Jones, S. / Zhang, H. / Donne, D.G. / Kaneko, K. / Groth, D. / Mehlhorn, I. / Prusiner, S.B. / Cohen, F.E.
History
DepositionNov 25, 1998Deposition site: BNL / Processing site: RCSB
SupersessionDec 2, 1998ID: 2PRP
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: 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: PROTEIN (PRION PROTEIN)


Theoretical massNumber of molelcules
Total (without water)16,2641
Polymers16,2641
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)25 / 100TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein PROTEIN (PRION PROTEIN) / SHA RPRP90-231


Mass: 16264.101 Da / Num. of mol.: 1 / Fragment: 90 - 231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Description: GENENTECH DERIVED VECTOR SYSTEM / Plasmid: STII VARIANT 4 (90 - 231) / Cellular location (production host): PERIPLASM / Gene (production host): ALKALINE PHOSPHATASE / Production host: Escherichia coli (E. coli) / Strain (production host): 27C7 / References: UniProt: P04273

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111N15 NOESY
121C13 NOESY
NMR detailsText: IONIC_STRENGTH: NULL PRESSURE: 1 ATM SOLVENT SYSTEM: 1MM PROTEIN, H2O, 20 MM SODIUM ACETATE THE 1H, 15N AND 13C RESONANCES WERE ASSIGNED USING TRIPLE RESONANCE NMR EXPERIMENTS HNCA, HNCACB, ...Text: IONIC_STRENGTH: NULL PRESSURE: 1 ATM SOLVENT SYSTEM: 1MM PROTEIN, H2O, 20 MM SODIUM ACETATE THE 1H, 15N AND 13C RESONANCES WERE ASSIGNED USING TRIPLE RESONANCE NMR EXPERIMENTS HNCA, HNCACB, CBCACONNH, HNCO, HCCH-TOCSY ACQUIRED ON 500 AND 600 MHZ SPECTROMETERS WITH UNIFORMLY 13C/15N-LABELED SAMPLE. DISTANCE RESTRAINTS WERE OBTAINED FROM 750 MHZ 15N-HSQC-NOESY AND 13C-HSQC- NOESY SPECTRA WITH 100MS MIXING TIME.

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Sample preparation

Sample conditionspH: 5.2 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AMXBrukerAMX6002
Varian UNITYPLUSVarianUNITYPLUS5003

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Processing

NMR software
NameDeveloperClassification
ARIAM. NILGESrefinement
XPLORA. T. BRUNGERrefinement
AMBER4.1P. A. KOLLMANrefinement
ARIAstructure solution
XPLORstructure solution
Amberstructure solution
RefinementMethod: NMR-RESTRAINED SIMULATED ANNEALING, MOLECULAR DYNAMICS, AND ENERGY MINIMIZATION.
Software ordinal: 1
Details: NMR DISTANCE RESTRAINTS WERE ASSIGNED WITH THE AID OF ARIA (AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT) PROCEDURE, RESULTING IN 2778 UNAMBIGUOUS AND 306 AMBIGUOUS DISTANCE RESTRAINTS. 63 ...Details: NMR DISTANCE RESTRAINTS WERE ASSIGNED WITH THE AID OF ARIA (AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT) PROCEDURE, RESULTING IN 2778 UNAMBIGUOUS AND 306 AMBIGUOUS DISTANCE RESTRAINTS. 63 J COUPLING CONSTANTS, AND 44 HYDROGEN BOND RESTRAINTS WERE ALSO USED IN THE STRUCTURE CALCULATIONS. 100 STRUCTURES WERE CALCULATED USING XPLOR NMR- RESTRAINED SIMULATED ANNEALING PROTOCOL. RESIDUES 112-231 OF THE 25 STRUCTURES WITH LOWEST TOTAL ENERGY WERE EACH SUBJECTED TO 25PS RESTRAINED MOLECULAR DYNAMICS SIMULATION IN A 6 ANGSTROM SHELL OF WATER FOLLOWED BY ENERGY MINIMIZATION USING AMBER4.1 FORCE FIELD. THE AVERAGE VIOLATION FOR DISTANCE RESTRAINTS IS 0.032A, AND FOR J COUPLING CONSTANTS IS 0.059HZ. THE AVERAGE BACKBONE ATOMIC RMSD TO THE MEAN STRUCTURE IS 0.67A FOR RESIDUES 125-227 OF THE 25 STRUCTURES. THE REFINEMENT HAS BEEN SUBMITTED TO BIOCHEMISTRY WITH THE TITLE "SOLUTION STRUCTURE OF SYRIAN HAMSTER PRION PROTEIN RPRP(90-231)". NOTE, LOWER RESOLUTION STRUCTURES PUBLISHED ON PNAS 94, 10086 (1997) WERE CALCULATED WITH THE PROGRAM DIANA DEVELOPED IN WUTHRICH'S LAB.RESIDUES 90-124 OF RPRP(90-231) ARE LARGELY UNSTRUCTURED. RESIDUES 90-111 WERE EXCLUDED IN THE FINAL STAGE OF STRUCTURE REFINEMENT. THE COORDINATES DEPOSITED TO PDB CONTAIN RESIDUES 125-228.
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 25

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