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- PDB-7wrs: Crystal structure of the chicken isoleucyl-tRNA synthetase 1 (IAR... -

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Basic information

Entry
Database: PDB / ID: 7wrs
TitleCrystal structure of the chicken isoleucyl-tRNA synthetase 1 (IARS1) UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1)
Components
  • Glutamyl-tRNA synthetase
  • Isoleucyl-tRNA synthetase
KeywordsTRANSLATION / Translation proteins / synthetase
Function / homology
Function and homology information


isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation ...isoleucine-tRNA ligase / isoleucine-tRNA ligase activity / isoleucyl-tRNA aminoacylation / regulation of long-chain fatty acid import into cell / glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / aminoacyl-tRNA deacylase activity / GAIT complex / cellular response to type II interferon / tRNA binding / negative regulation of translation / RNA binding / ATP binding / metal ion binding / membrane / cytosol
Similarity search - Function
Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / 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 ...Isoleucine-tRNA ligase, type 2 / Isoleucyl tRNA synthetase type 2, anticodon-binding domain / Isoleucine-tRNA ligase / 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 Ia / tRNA synthetases class I (I, L, M and V) / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding / Anticodon-binding domain of tRNA ligase / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / 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
Isoleucine--tRNA ligase / Bifunctional glutamate/proline--tRNA ligase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 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
B: Isoleucyl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)94,2902
Polymers94,2902
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-12 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.020, 155.550, 44.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-826-

HOH

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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: Protein Isoleucyl-tRNA synthetase / tRNA synthetase_I


Mass: 33130.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: IARS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q2UG33, isoleucine-tRNA ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 0.84 M NaH2PO4, 1.76 M K2HPO4, and 0.1 M sodium acetate, pH 4.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.2782 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 2.4→77.8 Å / Num. obs: 39660 / % possible obs: 100 % / Redundancy: 622.9 % / Biso Wilson estimate: 50.62 Å2 / CC1/2: 0.995 / CC star: 0.999 / R split: 0.1438 / Net I/σ(I): 5.2
Reflection shellResolution: 2.4→2.44 Å / Num. unique obs: 3908 / R split: 0.649
Serial crystallography measurementCollection time total: 12 hours / Collimation: Kirkpatrick-Baez mirrors / Pulse duration: 20 fsec. / Pulse photon energy: 9.7 keV
Serial crystallography sample deliveryDescription: fixed target / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.14-3260_1069refinement
PHENIX1.14-3260_1069refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R3Z

4r3z


Resolution: 2.4→71.51 Å / SU ML: 0.3439 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9538 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 1987 5.01 %
Rwork0.1914 37645 -
obs0.194 39632 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.59 Å2
Refinement stepCycle: LAST / Resolution: 2.4→71.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6358 0 0 26 6384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096484
X-RAY DIFFRACTIONf_angle_d0.9788776
X-RAY DIFFRACTIONf_chiral_restr0.0565990
X-RAY DIFFRACTIONf_plane_restr0.00611127
X-RAY DIFFRACTIONf_dihedral_angle_d7.25693969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.36921400.3232682X-RAY DIFFRACTION100
2.46-2.530.33911370.29732600X-RAY DIFFRACTION99.96
2.53-2.60.35841430.27532687X-RAY DIFFRACTION100
2.6-2.680.32911400.26082595X-RAY DIFFRACTION100
2.68-2.780.29471300.26352687X-RAY DIFFRACTION99.96
2.78-2.890.32411480.25882626X-RAY DIFFRACTION100
2.89-3.020.34041420.23022655X-RAY DIFFRACTION100
3.02-3.180.26771430.21282709X-RAY DIFFRACTION100
3.18-3.380.27721390.20492668X-RAY DIFFRACTION100
3.38-3.640.25711340.18262683X-RAY DIFFRACTION100
3.64-4.010.20611530.16452697X-RAY DIFFRACTION100
4.01-4.590.18551380.13542713X-RAY DIFFRACTION100
4.59-5.780.18221460.15552758X-RAY DIFFRACTION100
5.78-71.510.2241540.17992885X-RAY DIFFRACTION99.09

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