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

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Basic information

Entry
Database: PDB / ID: 2hrk
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 / sequence-specific mRNA binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity ...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 / sequence-specific mRNA binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / mRNA binding / mitochondrion / ATP binding / cytoplasm / cytosol
Similarity search - Function
Glutaredoxin - #70 / : / Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), anti-codon binding domain ...Glutaredoxin - #70 / : / Glutamine-tRNA ligase, alpha-bundle domain superfamily / : / Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / : / Nuclear-export cofactor Arc1p / Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain / : / tRNA synthetases class I (E and Q), 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: 2.05 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 20, 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 ...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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8043
Polymers36,7682
Non-polymers351
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.320, 86.310, 47.120
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is the binary 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 30-35 % PEG 3350, 0.3-0.5 M NaSCN, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 29, 2006 / Details: Osmic VariMax Multilayer
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.05→45 Å / Num. obs: 20000 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.038 / Net I/σ(I): 27.45
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5.75 / Num. unique all: 1396 / Rsym value: 0.28 / % possible all: 100

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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: 2.05→45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.252 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.221 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25552 1019 5.1 %RANDOM
Rwork0.19065 ---
all0.19386 18999 --
obs0.19386 18982 99.91 %-
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: 26.461 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20.31 Å2
2---0.57 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 1 274 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222355
X-RAY DIFFRACTIONr_bond_other_d0.0010.021545
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9593197
X-RAY DIFFRACTIONr_angle_other_deg0.85533813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1185296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84425.52196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92115417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.71157
X-RAY DIFFRACTIONr_chiral_restr0.0610.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022576
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.2160.2617
X-RAY DIFFRACTIONr_nbd_other0.180.21645
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21196
X-RAY DIFFRACTIONr_nbtor_other0.0850.21156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1110.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.224
X-RAY DIFFRACTIONr_mcbond_it0.5851.51594
X-RAY DIFFRACTIONr_mcbond_other0.0861.5597
X-RAY DIFFRACTIONr_mcangle_it0.97822400
X-RAY DIFFRACTIONr_scbond_it1.2283959
X-RAY DIFFRACTIONr_scangle_it1.8984.5797
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 87 -
Rwork0.242 1396 -
obs--99.93 %

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