[English] 日本語
Yorodumi
- PDB-2pid: Crystal structure of human mitochondrial tyrosyl-tRNA synthetase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pid
TitleCrystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog
ComponentsTyrosyl-tRNA synthetase
KeywordsLIGASE / AMINOACYL-TRNA SYNTHETASE / PROTEIN-SUBSTRATE COMPLEX / ATP-binding / Mitochondrion / Nucleotide-binding / Protein biosynthesis
Function / homology
Function and homology information


mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation ...mitochondrial tyrosyl-tRNA aminoacylation / L-tyrosine binding / tRNA aminoacylation / Mitochondrial tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / tRNA binding / nuclear body / mitochondrial matrix / translation / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / cytosol
Similarity search - Function
Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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 ...Tyrosine-tRNA ligase, bacterial-type / Tyrosine-tRNA ligase / Tyrosyl-Transfer RNA Synthetase / Tyrosyl-Transfer RNA Synthetase / 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 / RNA-binding S4 domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / Tyrosine--tRNA ligase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J.
Citation
Journal: Structure / Year: 2007
Title: Crystal Structure of Human Mitochondrial Tyrosyl-tRNA Synthetase Reveals Common and Idiosyncratic Features.
Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Sauter, C. / Rudinger-Thirion, J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Tyrosyl-tRNA synthetase: the first crystallization of a human mitochondrial aminoacyl-tRNA synthetase
Authors: Bonnefond, L. / Frugier, M. / Touze, E. / Lorber, B. / Florentz, C. / Giege, R. / Rudinger-Thirion, J. / Sauter, C.
History
DepositionApr 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,9444
Polymers79,9252
Non-polymers1,0192
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-21 kcal/mol
Surface area27180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.000, 62.400, 194.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tyrosyl-tRNA synthetase / Tyrosine-tRNA ligase / TyrRS


Mass: 39962.371 Da / Num. of mol.: 2 / Fragment: Residues 28-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YARS2 / Plasmid: pQE70-mt-TyrRS-[Delta]S4 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: Q9Y2Z4, tyrosine-tRNA ligase
#2: Chemical ChemComp-YSA / 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE / TYROSYLADENYLATE


Mass: 509.493 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O8S / Details: 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 3 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6, 100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 34168 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 19.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.427 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VBM

1vbm


Resolution: 2.2→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2251160.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1700 5 %RANDOM
Rwork0.193 ---
obs0.193 34156 99.6 %-
all-34156 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.68 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.6 Å20 Å20 Å2
2--3.12 Å20 Å2
3----10.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5102 0 70 90 5262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.832
X-RAY DIFFRACTIONc_mcangle_it3.842.5
X-RAY DIFFRACTIONc_scbond_it4.22.5
X-RAY DIFFRACTIONc_scangle_it5.83
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.309 171 5.2 %
Rwork0.228 3132 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3YSA.PARAMYSA.TOP

+
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