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- PDB-6kie: Crystal structure of human leucyl-tRNA synthetase, Leu-AMS-bound form -

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Basic information

Entry
Database: PDB / ID: 6kie
TitleCrystal structure of human leucyl-tRNA synthetase, Leu-AMS-bound form
ComponentsLeucine--tRNA ligase, cytoplasmic
KeywordsLIGASE / leucyl-tRNA synthetase / Leu-AMS-bound form
Function / homology
Function and homology information


glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Selenoamino acid metabolism / leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / cellular response to leucine starvation / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / cellular response to L-leucine ...glutamine-tRNA ligase activity / glutaminyl-tRNA aminoacylation / Selenoamino acid metabolism / leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / cellular response to leucine starvation / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / cellular response to L-leucine / tRNA aminoacylation for protein translation / aminoacyl-tRNA deacylase activity / endomembrane system / positive regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to amino acid starvation / GTPase activator activity / cellular response to amino acid stimulus / lysosome / nuclear body / endoplasmic reticulum / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / : / Leucine--tRNA ligase, ubiquitin-like domain / Leucine--tRNA ligase, RagD-binding domain / Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / 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 ...: / : / Leucine--tRNA ligase, ubiquitin-like domain / Leucine--tRNA ligase, RagD-binding domain / Leucyl-tRNA synthetase, class Ia, archaeal/eukaryotic cytosolic / 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 I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
LEUCINE / 5'-O-(L-leucylsulfamoyl)adenosine / PHOSPHATE ION / Leucine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsKim, S. / Son, J. / Kim, S. / Hwang, K.Y.
CitationJournal: Cell Rep / Year: 2021
Title: Leucine-sensing mechanism of leucyl-tRNA synthetase 1 for mTORC1 activation.
Authors: Kim, S. / Yoon, I. / Son, J. / Park, J. / Kim, K. / Lee, J.H. / Park, S.Y. / Kang, B.S. / Han, J.M. / Hwang, K.Y. / Kim, S.
History
DepositionJul 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8796
Polymers123,0031
Non-polymers8765
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.774, 138.774, 448.843
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 123003.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARS1, KIAA1352, LARS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2J5, leucine-tRNA ligase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N7O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
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: 4.63 Å3/Da / Density % sol: 78.89 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES (pH 7.1), 0.42 M Ammonium sulfate, 24% PEG3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 46132 / % possible obs: 96.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.043 / Rrim(I) all: 0.119 / Χ2: 2.59 / Net I/σ(I): 10.4 / Num. measured all: 280543
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.153.30.42321710.0780.250.4950.8593
3.15-3.213.90.43522430.0720.2370.4990.88296.5
3.21-3.2740.41922510.2060.2240.4780.91297.3
3.27-3.344.10.40722800.3740.2140.4631.01296.8
3.34-3.414.30.39222560.4970.1990.4421.05196.5
3.41-3.494.50.36322820.7690.180.4071.20696.8
3.49-3.584.70.33922700.7780.160.3771.33996.8
3.58-3.6850.30522660.8870.1380.3371.45896.1
3.68-3.785.40.28822560.9130.1240.3151.59796.3
3.78-3.915.70.24422860.9630.1010.2651.93697.3
3.91-4.046.10.21723020.9760.0860.2342.1197
4.04-4.216.60.19322940.9870.0740.2072.30595.9
4.21-4.47.10.16322810.9910.0590.1742.7196.4
4.4-4.637.60.14523160.9930.0520.1552.98596.7
4.63-4.927.70.13123290.9940.0460.143.34797.5
4.92-5.37.90.12523420.9950.0440.1323.35697.2
5.3-5.8380.11723900.9960.0410.1243.36497.8
5.83-6.678.40.09723930.9960.0330.1033.58497.5
6.67-8.48.60.06924520.9980.0230.0733.91197.9
8.4-507.90.05624720.9960.020.064.04390.9

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wz2

1wz2


Resolution: 3.15→46.848 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 29.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1901 4.34 %
Rwork0.2291 41916 -
obs0.23 43817 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.13 Å2 / Biso mean: 96.6088 Å2 / Biso min: 32.01 Å2
Refinement stepCycle: final / Resolution: 3.15→46.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8112 0 46 75 8233
Biso mean--73.45 82.71 -
Num. residues----1005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.15-3.22880.42911330.4045292597
3.2288-3.3160.42851330.3789293197
3.316-3.41360.35821320.3548291397
3.4136-3.52370.33231330.331294097
3.5237-3.64960.30861340.2976295596
3.6496-3.79570.29761320.2702291697
3.7957-3.96840.26221370.2434298897
3.9684-4.17740.23231320.2251294496
4.1774-4.4390.25221350.195297097
4.439-4.78140.20021360.1813299897
4.7814-5.2620.20931370.1953303298
5.262-6.02210.24991410.2121308998
6.0221-7.5820.20171410.1942312598
7.582-46.8480.18781450.1675319093

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