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- PDB-2hsm: Structural basis of yeast aminoacyl-tRNA synthetase complex forma... -

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Basic information

Entry
Database: PDB / ID: 2hsm
TitleStructural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Components
  • GU4 nucleic-binding protein 1
  • Glutamyl-tRNA synthetase, cytoplasmic
KeywordsLigase/RNA Binding Protein / protein complex protein interaction GST-fold / Ligase-RNA Binding Protein COMPLEX
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule ...methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / mRNA binding / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Glutaredoxin - #70 / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain ...Glutaredoxin - #70 / Glutamine-tRNA ligase, alpha-bundle domain superfamily / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / tRNA synthetases class I (E and Q), anti-codon binding domain / Glutamyl/glutaminyl-tRNA synthetase / Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain / tRNA synthetases class I (E and Q), catalytic domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 Yfyf (Class Pi); Chain A, domain 2 / 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 / Nucleic acid-binding, OB-fold / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutamate--tRNA ligase, cytoplasmic / tRNA-aminoacylation cofactor ARC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSimader, H. / Suck, D.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes.
Authors: Simader, H. / Hothorn, M. / Kohler, C. / Basquin, J. / Simos, G. / Suck, D.
History
DepositionJul 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl-tRNA synthetase, cytoplasmic
B: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)36,7682
Polymers36,7682
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.380, 87.460, 52.800
Angle α, β, γ (deg.)90.00, 92.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the heterodimeric complex. The asymmetric unit contains one biological unit.

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Components

#1: Protein Glutamyl-tRNA synthetase, cytoplasmic / Glutamate-tRNA ligase / GluRS / P85


Mass: 22765.432 Da / Num. of mol.: 1 / Fragment: residues 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GUS1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46655, glutamate-tRNA ligase
#2: Protein GU4 nucleic-binding protein 1 / G4p1 protein / P42 / ARC1 protein


Mass: 14002.878 Da / Num. of mol.: 1 / Fragment: residues 1-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARC1 / Plasmid: pETm derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46672

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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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293 K / pH: 7.2
Details: 30-35 % PEG 3350, 0.3-0.5 M NaSCN, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54179
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 2005
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7417 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.08 / Net I/σ(I): 13.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.67 / Rsym value: 0.324 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HRA PDB ENTRY 2HQT

2hra

2hqt


Resolution: 3→52.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.501 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 342 4.6 %RANDOM
Rwork0.195 ---
obs0.198 7075 98.1 %-
all-7210 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å2-0.22 Å2
2---0.15 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 3→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 0 0 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222362
X-RAY DIFFRACTIONr_bond_other_d0.0010.021546
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.963207
X-RAY DIFFRACTIONr_angle_other_deg0.92633819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16925.62596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47215416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.193157
X-RAY DIFFRACTIONr_chiral_restr0.0660.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
X-RAY DIFFRACTIONr_nbd_refined0.2470.2627
X-RAY DIFFRACTIONr_nbd_other0.1840.21594
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21159
X-RAY DIFFRACTIONr_nbtor_other0.090.21239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.431.51559
X-RAY DIFFRACTIONr_mcbond_other0.0491.5600
X-RAY DIFFRACTIONr_mcangle_it0.76722418
X-RAY DIFFRACTIONr_scbond_it0.7213940
X-RAY DIFFRACTIONr_scangle_it1.1514.5789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 16 -
Rwork0.273 412 -
obs--79.55 %

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