[English] 日本語
Yorodumi
- PDB-2kcy: SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S8E FROM Methanothermobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kcy
TitleSOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S8E FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET TR71D
Components30S ribosomal protein S8e
KeywordsRIBOSOMAL PROTEIN / RIBOSOMAL PROTEIN S8E / rsp8e / RDC / NESG / BETA / Ribonucleoprotein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Thrombin, subunit H - #310 / Ribosomal protein S8e, archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S8e / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Thrombin, subunit H / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Small ribosomal subunit protein eS8
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsLiu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. ...Liu, G. / Rossi, P. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B.C. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S8E FROM Methanothermobacter thermautotrophicus, NORTHEASTSTRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET TR71D
Authors: Liu, G. / Rossi, P. / Montelione, G.T.
History
DepositionDec 30, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 30S ribosomal protein S8e


Theoretical massNumber of molelcules
Total (without water)11,0411
Polymers11,0411
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein 30S ribosomal protein S8e


Mass: 11041.483 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: rps8e, MTH_207 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / References: UniProt: O26309

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: further refined with RDC data
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-15N HSQC
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1633D 1H-13C NOESY
1713D HNCO
1813D CBCA(CO)NH
1913D HN(CA)CB
11013D C(CO)NH
11113D HBHA(CO)NH
11222D 1H-15N HSQC
11322D 1H-13C HSQC
11432D 1H-13C HSQC
11542D 1H-15N HSQC TROSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.94 mM [U-100% 13C; U-100% 15N] protein-1, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-10% 13C; U-99% 15N] protein-2, 95% H2O/5% D2O95% H2O/5% D2O
30.94 mM [U-100% 13C; U-100% 15N] protein-3, 100% D2O100% D2O
41.0 mM [U-10% 13C; U-99% 15N] protein-4, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.94 mMprotein-1[U-100% 13C; U-100% 15N]1
1.0 mMprotein-2[U-10% 13C; U-99% 15N]2
0.94 mMprotein-3[U-100% 13C; U-100% 15N]3
1.0 mMprotein-4[U-10% 13C; U-99% 15N]4
Sample conditionsIonic strength: n.a. / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
GE AvanceGEAVANCE8002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
AutoStructureHuang, Tejero, Powers and Montelionerefinement
AutoStructureHuang, Tejero, Powers and Montelionedata analysis
AutoStructureHuang, Tejero, Powers and Montelionepeak picking
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoAssignZimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssignZimmerman, Moseley, Kulikowski and Montelionepeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
PSVSBhattacharya and Montelionedata analysis
PSVSBhattacharya and Montelionerefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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