[English] 日本語
Yorodumi
- PDB-1b10: SOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEI... -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / 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 / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / terminal bouton / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / presynapse / signaling receptor activity / amyloid-beta binding / microtubule binding / protease 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 / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prion/Doppel protein, beta-ribbon domain / Major Prion Protein / 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 protein, beta-ribbon domain / Major Prion Protein / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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.

-
Sample preparation

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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more