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- PDB-7wru: Crystal structure of the apo chicken glutamyl-tRNA synthetase 1 (... -

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Basic information

Entry
Database: PDB / ID: 7wru
TitleCrystal structure of the apo chicken glutamyl-tRNA synthetase 1 (EARS1)
ComponentsGlutamyl-tRNA synthetase
KeywordsTRANSLATION / Vertabrate / tRNA synthetase
Function / homology
Function and homology information


regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / cellular response to type II interferon ...regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / glutamyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / GAIT complex / cellular response to type II interferon / negative regulation of translation / RNA binding / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / 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 ...Glutamyl-tRNA synthetase, archaeal/eukaryotic cytosolic / 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 / 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. / 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 / S15/NS1, RNA-binding
Similarity search - Domain/homology
: / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChung, S. / Cho, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1.
Authors: Chung, S. / Kang, M.S. / Alimbetov, D.S. / Mun, G.I. / Yunn, N.O. / Kim, Y. / Kim, B.G. / Wie, M. / Lee, E.A. / Ra, J.S. / Oh, J.M. / Lee, D. / Lee, K. / Kim, J. / Han, S.H. / Kim, K.T. / ...Authors: Chung, S. / Kang, M.S. / Alimbetov, D.S. / Mun, G.I. / Yunn, N.O. / Kim, Y. / Kim, B.G. / Wie, M. / Lee, E.A. / Ra, J.S. / Oh, J.M. / Lee, D. / Lee, K. / Kim, J. / Han, S.H. / Kim, K.T. / Chung, W.K. / Nam, K.H. / Park, J. / Lee, B. / Kim, S. / Zhao, W. / Ryu, S.H. / Lee, Y.S. / Myung, K. / Cho, Y.
History
DepositionJan 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamyl-tRNA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5613
Polymers61,1601
Non-polymers4012
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-25 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.044, 41.762, 92.186
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glutamyl-tRNA synthetase / tRNA synthetase_E


Mass: 61159.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: RCJMB04_20b9 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5ZJ86, proline-tRNA ligase, glutamate-tRNA ligase
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 85 mM HEPES (pH 7.5), 8.5% isopropanol, 15% glycerol, 40 mM NaF and 15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1.0094 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.5→45.36 Å / Num. obs: 23252 / % possible obs: 98.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.66 Å2 / CC1/2: 0.976 / Rrim(I) all: 0.386 / Net I/σ(I): 8.11
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2352 / CC1/2: 0.612 / Rrim(I) all: 2.885

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3Z

4r3z


Resolution: 2.5→45.36 Å / SU ML: 0.3663 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.6099 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 1159 4.99 %
Rwork0.2239 42347 -
obs0.2262 23252 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 2 3 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01194084
X-RAY DIFFRACTIONf_angle_d1.13355513
X-RAY DIFFRACTIONf_chiral_restr0.0574598
X-RAY DIFFRACTIONf_plane_restr0.0068710
X-RAY DIFFRACTIONf_dihedral_angle_d9.5932495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.34311420.2922670X-RAY DIFFRACTION99.86
2.55-2.610.33611540.29592710X-RAY DIFFRACTION99.31
2.61-2.680.35691330.28562637X-RAY DIFFRACTION99.46
2.68-2.750.36881530.28032681X-RAY DIFFRACTION99.26
2.75-2.830.29891380.26512643X-RAY DIFFRACTION99.36
2.83-2.920.31211400.25322640X-RAY DIFFRACTION98.97
2.92-3.030.29171590.24282661X-RAY DIFFRACTION98.95
3.03-3.150.27481430.24562669X-RAY DIFFRACTION99.29
3.15-3.290.29831100.24982676X-RAY DIFFRACTION98.17
3.29-3.470.32781230.23112563X-RAY DIFFRACTION94.91
3.47-3.680.28781390.21382516X-RAY DIFFRACTION95.4
3.68-3.970.23251530.20352684X-RAY DIFFRACTION99.54
3.97-4.370.22071180.18062696X-RAY DIFFRACTION99.65
4.37-50.23531440.18162653X-RAY DIFFRACTION99.43
5-6.290.27041480.21382614X-RAY DIFFRACTION97.15
6.29-45.360.18221290.2022634X-RAY DIFFRACTION97.49

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