[English] 日本語
Yorodumi
- PDB-1r6t: crystal structure of human tryptophanyl-tRNA synthetase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r6t
Titlecrystal structure of human tryptophanyl-tRNA synthetase
ComponentsTryptophanyl-tRNA synthetase
KeywordsLIGASE / Class Ic tRNA synthetase / Rossmann fold catalytical domain / anticodon recognition domain / bound Trp-AMP
Function / homology
Function and homology information


tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation ...tryptophan-tRNA ligase / tryptophanyl-tRNA aminoacylation / tryptophan-tRNA ligase activity / kinase inhibitor activity / Cytosolic tRNA aminoacylation / regulation of angiogenesis / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / angiogenesis / translation / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / protein homodimerization activity / protein-containing complex / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class Ic ...WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Tryptophan-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / S15/NS1, RNA-binding / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Helix Hairpins / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHANYL-5'AMP / Tryptophan--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsYang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Ribas de Pouplana, L. / Schimmel, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains
Authors: Yang, X.-L. / Otero, F.J. / Skene, R.J. / McRee, D.E. / Schimmel, P. / Ribas De Pouplana, L.
History
DepositionOct 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tryptophanyl-tRNA synthetase
B: Tryptophanyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4695
Polymers108,7512
Non-polymers7183
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-25 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.146, 95.713, 98.506
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Tryptophanyl-tRNA synthetase / Tryptophan--tRNA ligase / TrpRS / IFP53 / hWRS


Mass: 54375.602 Da / Num. of mol.: 2 / Mutation: S213G, Y214D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WARS / Plasmid: pET20b+ / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P23381, tryptophan-tRNA ligase
#2: Chemical ChemComp-TYM / TRYPTOPHANYL-5'AMP


Mass: 533.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N7O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.32
Details: PEG 8K, Mes, pH 6.32, VAPOR DIFFUSION, SITTING DROP, temperature 279K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %PEG80001reservoir
20.1 Msodium-MES1reservoirpH6.32
310 mMHEPES1droppH7.5
420 mM1dropKCl
50.02 %1dropNaN3
62 mM2-mercaptoethanol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2002
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 162039 / Num. obs: 153937 / % possible obs: 95 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 13.87
Reflection shellResolution: 2.1→2.17 Å / % possible all: 87.3
Reflection
*PLUS
Num. obs: 82479 / % possible obs: 96.5 %
Reflection shell
*PLUS
% possible obs: 87.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1

-
Processing

Software
NameClassification
Blu-Icedata collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2386 6915 Random
Rwork0.208 --
all0.2082 162215 -
obs0.2082 139484 -
Solvent computationBsol: 45.2541 Å2 / ksol: 0.341653 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.024 Å20 Å2-8.367 Å2
2---3.98 Å20 Å2
3---0.956 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6435 0 49 294 6778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna.param
X-RAY DIFFRACTION3WPA.param
X-RAY DIFFRACTION4goln.param
X-RAY DIFFRACTION5water_rep.param
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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