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- PDB-5bmu: The crystal structure of the GST-like domains complex of AIMP3-EP... -

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Basic information

Entry
Database: PDB / ID: 5bmu
TitleThe crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S
Components
  • Eukaryotic translation elongation factor 1 epsilon-1
  • Glutamate--tRNA ligase
KeywordsTRANSLATION/LIGASE / AIMP3 / EPRS / GST-like domain / TRANSLATION-LIGASE complex
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation ...regulation of long-chain fatty acid import into cell / Selenoamino acid metabolism / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / tRNA modification in the nucleus and cytosol / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / cellular response to type II interferon / RNA stem-loop binding / cellular response to insulin stimulus / positive regulation of cellular senescence / GTPase binding / negative regulation of translation / positive regulation of apoptotic process / translation / ribonucleoprotein complex / negative regulation of cell population proliferation / nucleolus / protein homodimerization activity / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #130 / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / WHEP-TRS domain / tRNA synthetases class I (E and Q), anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / 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 / 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 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. / 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 / Glutaredoxin / S15/NS1, RNA-binding / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation elongation factor 1 epsilon-1 / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCho, 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.Y. / Kim, Y.G. / Guo, M. / Jung, H.S. / Kang, B.S. / Kim, S.
History
DepositionMay 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation elongation factor 1 epsilon-1
B: Glutamate--tRNA ligase
C: Eukaryotic translation elongation factor 1 epsilon-1
D: Glutamate--tRNA ligase
E: Eukaryotic translation elongation factor 1 epsilon-1
F: Glutamate--tRNA ligase
G: Eukaryotic translation elongation factor 1 epsilon-1
H: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)154,9558
Polymers154,9558
Non-polymers00
Water1086
1
A: Eukaryotic translation elongation factor 1 epsilon-1
B: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,7392
Polymers38,7392
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Eukaryotic translation elongation factor 1 epsilon-1
D: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,7392
Polymers38,7392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Eukaryotic translation elongation factor 1 epsilon-1
F: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,7392
Polymers38,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Eukaryotic translation elongation factor 1 epsilon-1
H: Glutamate--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)38,7392
Polymers38,7392
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.063, 92.063, 185.948
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Eukaryotic translation elongation factor 1 epsilon-1 / AIMP3 / Aminoacyl tRNA synthetase complex-interacting multifunctional protein 3 / Elongation factor ...AIMP3 / Aminoacyl tRNA synthetase complex-interacting multifunctional protein 3 / Elongation factor p18 / Multisynthase complex auxiliary component p18


Mass: 19428.141 Da / Num. of mol.: 4 / Fragment: UNP residues 1-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEF1E1, AIMP3, P18 / Production host: Escherichia coli (E. coli) / References: UniProt: O43324
#2: Protein
Glutamate--tRNA ligase


Mass: 19310.699 Da / Num. of mol.: 4 / Fragment: EPRS GST-like domain, UNP residues 1-175 / Mutation: C92S C105S C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPRS / Production host: Escherichia coli (E. coli) / References: UniProt: P07814, glutamate-tRNA ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: Ammonium sulfate, Sodium chloride, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 53953 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 5.4 % / Rsym value: 0.157 / Net I/σ(I): 16.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BVX

4bvx


Resolution: 2.6→48.93 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.867 / SU B: 2.679 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16957 1980 3.7 %RANDOM
Rwork0.13801 ---
obs0.13917 51915 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.298 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10457 0 0 6 10463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910687
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210150
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.94214525
X-RAY DIFFRACTIONr_angle_other_deg1.049323282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.73451322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53124.917484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.165151811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6091536
X-RAY DIFFRACTIONr_chiral_restr0.0850.21687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212113
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022501
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_it2.0153.2665312
X-RAY DIFFRACTIONr_mcbond_other2.0133.2655311
X-RAY DIFFRACTIONr_mcangle_it3.4424.8926623
X-RAY DIFFRACTIONr_mcangle_other3.4424.8936624
X-RAY DIFFRACTIONr_scbond_it1.3133.1275375
X-RAY DIFFRACTIONr_scbond_other1.3133.1255373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2184.7037901
X-RAY DIFFRACTIONr_long_range_B_refined4.99824.67812009
X-RAY DIFFRACTIONr_long_range_B_other4.99824.68212010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.091 140 -
Rwork0.075 3754 -
obs--97.77 %

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