[English] 日本語
Yorodumi
- PDB-1rqs: NMR structure of C-terminal domain of ribosomal protein L7 from E.coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rqs
TitleNMR structure of C-terminal domain of ribosomal protein L7 from E.coli
Components50S ribosomal protein L7/L12
KeywordsRIBOSOME / protein L7/L12
Function / homology
Function and homology information


large ribosomal subunit / ribosome binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / mRNA binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli O6 (bacteria)
Escherichia coli O157:H7 (bacteria)
Shigella flexneri (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics in torsion angle space
AuthorsBocharov, E.V. / Sobol, A.G. / Pavlov, K.V. / Korzhnev, D.M. / Jaravine, V.A. / Gudkov, A.T. / Arseniev, A.S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: From structure and dynamics of protein L7/L12 to molecular switching in ribosome.
Authors: Bocharov, E.V. / Sobol, A.G. / Pavlov, K.V. / Korzhnev, D.M. / Jaravine, V.A. / Gudkov, A.T. / Arseniev, A.S.
History
DepositionDec 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 50S ribosomal protein L7/L12


Theoretical massNumber of molelcules
Total (without water)7,5741
Polymers7,5741
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 / 200structures with the least restraint violations,target function
RepresentativeModel #9lowest energy

-
Components

#1: Protein 50S ribosomal protein L7/L12 / L8


Mass: 7573.641 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli, Escherichia coli O6, Escherichia coli O157:H7, Shigella flexneri
Genus: Escherichia, Escherichia, Escherichia, Shigella / Species: , Escherichia coli, Escherichia coli, / Strain: , O6, O157:H7, / Plasmid: pPR1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 / References: UniProt: P0A7K2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1222D NOESY
1313D 15N-HNHB
14115N-HMQCJ
15315N-JNH MODULATED HSQC
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C90% H2O/10% D2O
21mM L7 dimer U-15N; 50mM phosphate buffer; 99.9% D2O; 30 C99.9% D2O
31mM L7 dimer U-15N; 50mM phosphate buffer; 90% H2O, 10% D2O; 30 C; Tobacco virus alignment medium90% H2O/10% D2O
Sample conditionsIonic strength: 0.15 / pH: 6.9 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.3bVARIAN USAcollection
XEASY1.2.11Bartels, C.data analysis
CYANA1.01Guntert, P.structure solution
FANTOM4Schaumann, T.refinement
RefinementMethod: simulated annealing, molecular dynamics in torsion angle space
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,target function
Conformers calculated total number: 200 / 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://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