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- PDB-9tju: Ternary complex of E. coli leucyl-tRNA synthetase bound to tRNA(l... -

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Basic information

Entry
Database: PDB / ID: 9tju
TitleTernary complex of E. coli leucyl-tRNA synthetase bound to tRNA(leu) and Leucinol in the editing state
Components
  • Leucine--tRNA ligase
  • tRNA(leu)
KeywordsRNA BINDING PROTEIN / Leucine tRNA ligase Antimicrobial target tRNA aminoacylation for protein translation
Function / homology
Function and homology information


leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA deacylase activity / ATP binding / cytosol
Similarity search - Function
Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) ...Leucyl-tRNA synthetase, editing domain / Leucyl-tRNA synthetase, editing domain / Leucine-tRNA ligase / 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 / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
ACETATE ION / 2-AMINO-4-METHYL-PENTAN-1-OL / TRIETHYLENE GLYCOL / : / RNA / RNA (> 10) / Leucine--tRNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsHoffmann, G. / Palencia, A.
Funding support France, European Union, 4items
OrganizationGrant numberCountry
Grenoble Instruct-ERIC Center (ISBG)27604 France
iNEXT-Discovery45625European Union
Agence Nationale de la Recherche (ANR)ANR-20-AMRB-0003 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0040 France
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: The Zn Domain Acts as a Dynamic Switch Coordinating Multiple-Step Aminoacylation in Bacterial Leucyl-tRNA Synthetase
Authors: Hoffmann, G. / Dulic, M. / Gruic-Sovulj, I. / Palencia, A.
History
DepositionDec 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase
B: tRNA(leu)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,2319
Polymers127,5692
Non-polymers6637
Water13,998777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.694, 119.545, 141.639
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein Leucine--tRNA ligase / Leucyl-tRNA synthetase / LeuRS


Mass: 99516.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli Leucyl tRNA synthetase / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: leuS, b0642, JW0637 / Production host: Escherichia coli (E. coli) / References: UniProt: P07813, leucine-tRNA ligase
#2: RNA chain tRNA(leu)


Mass: 28052.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E. coli tRNA(Leu) isoacceptor UAA / Source: (gene. exp.) Escherichia coli (E. coli)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 1231762938

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Non-polymers , 5 types, 784 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DCL / 2-AMINO-4-METHYL-PENTAN-1-OL / LEUCINOL


Type: peptide-like / Mass: 117.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Acetate pH5.0, 0.2M Ammonium Chloride, 20-24% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2024 / Details: Vertical CRL / Horizontal CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.782→70.82 Å / Num. obs: 101703 / % possible obs: 96.3 % / Redundancy: 13.2 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Net I/σ(I): 15.4
Reflection shellResolution: 1.782→1.917 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.548 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5085 / CC1/2: 0.643 / Rpim(I) all: 0.455 / Rrim(I) all: 1.615 / % possible all: 66.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC20240123data reduction
STARANISOdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.782→35.41 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 5083 -RANDOM
Rwork0.2033 96601 --
obs0.2049 101684 81.6 %-
Displacement parametersBiso mean: 37.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.7008 Å20 Å20 Å2
2--1.6731 Å20 Å2
3----0.9723 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 1.782→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 1711 44 777 9049
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098666HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8512133HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2736SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1228HARMONIC5
X-RAY DIFFRACTIONt_it8666HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1174SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7039SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion16.72
LS refinement shellResolution: 1.782→1.87 Å
RfactorNum. reflection% reflection
Rfree0.2838 95 -
Rwork0.2832 1939 -
obs--12 %
Refinement TLS params.

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)
10.44020.43770.17881.2230.364600.05450.0869-0.0275-0.1509-0.1876-0.1949-0.04720.10280.1331-0.02680.03030.03230.08240.0913-0.079410.7262-6.65668.8499
20.074-0.00860.07360.17760.06380.1715-0.03040.01340.0398-0.06310.01630.0047-0.01420.02050.0141-0.02850.01350.00980.0160.0145-0.02570.276817.639419.2105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B1 - 76
2X-RAY DIFFRACTION2{ A|* }A1 - 860
3X-RAY DIFFRACTION2{ A|* }A901 - 909

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