[English] 日本語
Yorodumi
- PDB-1d2d: Hamster EprS second repeated element. NMR, 5 structures -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1d2d
TitleHamster EprS second repeated element. NMR, 5 structures
ComponentsTRNA SYNTHETASEAminoacyl tRNA synthetase
KeywordsLIGASE / TRNA SYNTHETASE (LIGASE) / PROTEIN TRANSCRIPTION
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / RNA stem-loop binding / GAIT complex ...regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / proline-tRNA ligase / glutamyl-tRNA aminoacylation / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / RNA stem-loop binding / GAIT complex / cellular response to type II interferon / cellular response to insulin stimulus / GTPase binding / negative regulation of translation / ribonucleoprotein complex / protein homodimerization activity / zinc ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Prolyl-tRNA synthetase, catalytic domain / Proline-tRNA ligase, class II, C-terminal / Prolyl-tRNA synthetase, C-terminal / Prolyl-tRNA synthetase, C-terminal / Proline-tRNA ligase, class IIa, archaeal-type / Prolyl-tRNA synthetase, class II / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Glutathione S-transferase, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / S15/NS1, RNA-binding / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
AuthorsCahuzac, B. / Berthonneau, E. / Birlirakis, N. / Guittet, E. / Mirande, M.
CitationJournal: EMBO J. / Year: 2000
Title: A recurrent RNA-binding domain is appended to eukaryotic aminoacyl-tRNA synthetases.
Authors: Cahuzac, B. / Berthonneau, E. / Birlirakis, N. / Guittet, E. / Mirande, M.
History
DepositionSep 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRNA SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)6,7221
Polymers6,7221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 40structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein TRNA SYNTHETASE / Aminoacyl tRNA synthetase / TRNA LIGASE


Mass: 6721.820 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus griseus (Chinese hamster) / Organ: OVARY CELLS / Plasmid: PET28B / Production host: Escherichia coli (E. coli)
References: UniProt: Q7SIA2, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-SEPARATED NOESY
131HNHA

-
Sample preparation

DetailsContents: 1.5 MM EPRS REPEAT U-15N; 20 MM POTASSIUM PHOSPHATE PH 7.0, 5 MM DITHIOTHREITOL, 0.5 MM NAN3;
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
Felix97MSI CORP.processing
XwinNMR2.5BRUKER CORP.collection
Gifa4DELSUC M.A.processing
DIANA1GUNTERT P.structure solution
X-PLOR3.1BRUNGER A.T.refinement
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 40 / Conformers submitted total number: 5

+
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