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- PDB-2hra: Crystal structures of the interacting domains from yeast glutamyl... -

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Basic information

Entry
Database: PDB / ID: 2hra
TitleCrystal structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA aminoacylation and nuclear export cofactor Arc1p reveal a novel function for an old fold
ComponentsGlutamyl-tRNA synthetase, cytoplasmic
KeywordsLIGASE / GST-fold
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / methionyl-tRNA aminoacylation / cytoplasmic stress granule / 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 / : / 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 / 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 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Glutamate--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSimader, H. / Hothorn, M. / Suck, D.
Citation
Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006
Title: Structures of the interacting domains from yeast glutamyl-tRNA synthetase and tRNA-aminoacylation and nuclear-export cofactor Arc1p reveal a novel function for an old fold.
Authors: Simader, H. / Hothorn, M. / Suck, D.
#1: Journal: To be Published
Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Authors: Simader, H. / Hothorn, M. / Koehler, 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: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Glutamyl-tRNA synthetase, cytoplasmic
B: Glutamyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,50546
Polymers45,9212
Non-polymers5,58444
Water4,882271
1
A: Glutamyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49921
Polymers22,9611
Non-polymers2,53820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamyl-tRNA synthetase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,00625
Polymers22,9611
Non-polymers3,04624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.959, 107.113, 167.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a monomer, two of which are contained in the asymmetric unit.

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Components

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


Mass: 22960.629 Da / Num. of mol.: 2
Fragment: N-terminal heteromerisation domain, residues 1-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GUS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46655, glutamate-tRNA ligase
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.8-1.9 M (NH4)2SO4, 200 mM NaI, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.97925
SYNCHROTRONSLS X06SA20.97912, 0.97934, 0.95372
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDDec 17, 2004
MARMOSAIC 225 mm CCD2CCDApr 29, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled channel-carved Si(111) mono-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2LN2 cooled fixed-exit Si(111) monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.979121
30.979341
40.953721
ReflectionResolution: 1.9→80 Å / Num. obs: 37390 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.073 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 5271 / Rsym value: 0.36 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 1.9→80 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.558 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.151 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26202 1892 5.1 %RANDOM
Rwork0.21408 ---
all0.21643 35521 --
obs0.21643 35496 99.93 %-
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: 24.734 Å2
Baniso -1Baniso -2Baniso -3
1-3.63 Å20 Å20 Å2
2---1.49 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 44 271 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222773
X-RAY DIFFRACTIONr_bond_other_d0.0010.021847
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9693753
X-RAY DIFFRACTIONr_angle_other_deg0.94534565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96525.888107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2315504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.84158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02506
X-RAY DIFFRACTIONr_nbd_refined0.2330.2667
X-RAY DIFFRACTIONr_nbd_other0.1970.21853
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21394
X-RAY DIFFRACTIONr_nbtor_other0.090.21430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3830.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4690.24
X-RAY DIFFRACTIONr_mcbond_it0.81.51793
X-RAY DIFFRACTIONr_mcbond_other0.2011.5720
X-RAY DIFFRACTIONr_mcangle_it1.34822852
X-RAY DIFFRACTIONr_scbond_it2.18531068
X-RAY DIFFRACTIONr_scangle_it3.3914.5901
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 143 -
Rwork0.272 2580 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69590.0628-0.78251.3122-0.22062.9891-0.01030.0463-0.06-0.21430.0247-0.0912-0.05360.0309-0.0144-0.0055-0.08140.0202-0.0518-0.0109-0.007329.408767.681765.598
21.45240.6241-1.09932.11270.0113.3248-0.13630.12830.0694-0.28050.1368-0.01870.0512-0.1359-0.0005-0.0828-0.0763-0.0105-0.0594-0.0026-0.032517.638140.773164.8826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 19819 - 198
2X-RAY DIFFRACTION2BB21 - 19321 - 193

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