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- PDB-6kqy: Crystal structure of human leucyl-tRNA synthetase, Leucine-bound form -

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Basic information

Entry
Database: PDB / ID: 6kqy
TitleCrystal structure of human leucyl-tRNA synthetase, Leucine-bound form
ComponentsLeucine--tRNA ligase, cytoplasmic
KeywordsLIGASE / leucyl-tRNA synthetase / leucine-bound structure
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 / tRNA aminoacylation for protein translation ...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 / tRNA aminoacylation for protein translation / cellular response to L-leucine / aminoacyl-tRNA deacylase activity / regulation of cell size / positive regulation of GTPase activity / positive regulation of TOR signaling / positive regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / endomembrane system / GTPase activator activity / cellular response to amino acid starvation / 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 / PHOSPHATE ION / Leucine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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
DepositionAug 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,4134
Polymers136,0551
Non-polymers3573
Water8,053447
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-2 kcal/mol
Surface area45880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.744, 123.744, 536.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1440-

HOH

21A-1543-

HOH

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Components

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


Mass: 136055.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs / Source: (gene. exp.) Homo sapiens (human) / Gene: LARS, KIAA1352 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2J5, leucine-tRNA ligase
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growTemperature: 293 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: 273 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: Mar 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 67806 / % possible obs: 93.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.06 / Rrim(I) all: 0.2 / Χ2: 2.155 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible allCC1/2
2.8-2.851.10.305690.3050.4310.5332.3
2.85-2.93.70.46227070.2540.5310.72789.50.07
2.9-2.964.40.47529770.2410.5370.74997.5
2.96-3.024.80.47129240.2260.5250.73697.70.002
3.02-3.085.30.47429630.2170.5240.759980.017
3.08-3.155.70.46829760.2050.5130.75398.30.024
3.15-3.235.90.45629550.1960.4990.738980.061
3.23-3.326.20.45129990.190.4920.75898.60.142
3.32-3.426.40.44130080.1820.4790.74898.70.098
3.42-3.536.60.44530070.180.4820.90498.50.176
3.53-3.656.90.40830430.1610.4410.78399.10.352
3.65-3.87.50.39830050.150.4270.89298.80.524
3.8-3.977.90.37730620.1360.4031.079990.719
3.97-4.1890.32730260.110.3471.01498.80.867
4.18-4.4410.20.2830930.0870.2941.199990.96
4.44-4.7912.10.24630870.0680.2551.453990.978
4.79-5.2712.90.22730940.0610.2361.59299.10.986
5.27-6.03140.22831410.0580.2361.81999.10.988
6.03-7.5917.40.16632130.0380.1712.751990.994
7.59-5022.40.08734630.0170.0896.43798.40.999

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wz2

1wz2


Resolution: 3.3→49.76 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2756 2362 3.48 %
Rwork0.2508 65444 -
obs0.2516 67806 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 225.72 Å2 / Biso mean: 48.6675 Å2 / Biso min: 9 Å2
Refinement stepCycle: final / Resolution: 3.3→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8088 0 23 449 8560
Biso mean--42.52 24.92 -
Num. residues----1002
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.370.31271370.27053763390097
3.37-3.440.35181350.26943825396096
3.44-3.520.31791360.27573777391396
3.52-3.610.2931360.27723784392097
3.61-3.710.30711390.2833802394197
3.71-3.820.30461390.28073830396998
3.82-3.940.31971350.27893825396097
3.94-4.080.31691370.26513850398798
4.08-4.240.33221380.27583860399899
4.24-4.440.25651400.26883897403799
4.44-4.670.27041400.2483854399499
4.67-4.960.22391460.2433914406099
4.96-5.340.31611340.25093875400999
5.34-5.880.281420.25023889403199
5.88-6.730.29831440.25873873401799
6.73-8.470.22571400.223139104050100
8.47-49.760.18411440.18773916406099

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