[English] 日本語
Yorodumi
- PDB-4bvx: Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bvx
TitleCrystal structure of the AIMP3-MRS N-terminal domain complex with I3C
Components
  • EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
  • METHIONINE--TRNA LIGASE, CYTOPLASMIC
KeywordsLIGASE / MRS
Function / homology
Function and homology information


Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / rRNA transcription ...Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / rRNA transcription / cellular response to platelet-derived growth factor stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / positive regulation of cellular senescence / tRNA binding / positive regulation of apoptotic process / translation / negative regulation of cell population proliferation / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Glutaredoxin / Glutaredoxin / S15/NS1, RNA-binding / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-I3C / Eukaryotic translation elongation factor 1 epsilon-1 / Methionine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCho, H.Y. / Seo, W.W. / Cho, H.J. / Kang, B.S.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Assembly of Multi-tRNA Synthetase Complex Via Heterotetrameric Glutathione Transferase-Homology Domains.
Authors: Cho, H.Y. / Maeng, S.J. / Cho, H.J. / Choi, Y.S. / Chung, J.M. / Lee, S. / Kim, H.K. / Kim, J.H. / Eom, C. / Kim, Y. / Guo, M. / Jung, H.S. / Kang, B.S. / Kim, S.
History
DepositionJun 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Dec 16, 2015Group: Database references / Other / Structure summary
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: METHIONINE--TRNA LIGASE, CYTOPLASMIC
B: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2165
Polymers43,5402
Non-polymers1,6773
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-6.8 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.284, 71.584, 116.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein METHIONINE--TRNA LIGASE, CYTOPLASMIC / METHIONYL-TRNA SYNTHETASE / METRS


Mass: 24060.424 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56192, methionine-tRNA ligase
#2: Protein EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1 / AIMP3 / AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN ELONGATION FACTOR P18 ...AIMP3 / AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN ELONGATION FACTOR P18 / MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P18


Mass: 19479.271 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-169 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43324
#3: Chemical ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H4I3NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.16 Å3/Da / Density % sol: 43.08 % / Description: NONE
Crystal growpH: 7.7
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 3350, 10 MM DTT, 100 MM HEPES, PH 7.7; THEN SOAKED IN 200 MM I3C.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43517 / % possible obs: 89.2 % / Observed criterion σ(I): -2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.62 / % possible all: 94.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→30.49 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.144 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. M1 TO L169 OF AIMP3 WITH ADDITIONAL GH SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE
RfactorNum. reflection% reflectionSelection details
Rfree0.24657 2189 5 %RANDOM
Rwork0.21681 ---
obs0.21833 41292 89.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.042 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 48 178 3175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023162
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9854334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9965405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83224.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8615535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3591518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212419
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 159 -
Rwork0.282 2935 -
obs--93.59 %

+
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