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- PDB-4bvx: Crystal structure of the AIMP3-MRS N-terminal domain complex with I3C -

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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 / cytoplasm / cytosol
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 Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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.

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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

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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 %

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