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- PDB-6kr7: Crystal structure of methylated human leucyl-tRNA synthetase, Leu... -

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Basic information

Entry
Database: PDB / ID: 6kr7
TitleCrystal structure of methylated human leucyl-tRNA synthetase, Leu-AMS-bound form
ComponentsLeucine--tRNA ligase, cytoplasmic
KeywordsLIGASE / leucyl-tRNA synthetase / Leu-AMS-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
Isoleucyl-tRNA Synthetase; Domain 1 - #20 / : / : / 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) / Isoleucyl-tRNA Synthetase; Domain 1 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain ...Isoleucyl-tRNA Synthetase; Domain 1 - #20 / : / : / 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) / Isoleucyl-tRNA Synthetase; Domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
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: 4 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 21, 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)136,7414
Polymers136,0551
Non-polymers6863
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-3 kcal/mol
Surface area45200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.818, 136.818, 437.266
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: 136055.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#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-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.34 Å3/Da / Density % sol: 76.07 %
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 130 mm / Detector: CCD / Date: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 20622 / % possible obs: 95.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.034 / Rrim(I) all: 0.112 / Χ2: 1.374 / Net I/σ(I): 6.7 / Num. measured all: 145569
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4-4.0740.3089760.5510.1530.3480.29993.9
4.07-4.144.30.3069820.7430.1450.3420.32893.4
4.14-4.224.30.3029610.680.1380.3360.36191.7
4.22-4.314.70.2799910.8170.1190.3060.43293.2
4.31-4.45.10.2669900.8250.1120.2920.49394.6
4.4-4.55.30.2669630.8810.1070.2890.693.4
4.5-4.625.50.24710100.910.0940.2660.66493.9
4.62-4.745.60.24110010.940.0940.2610.6793.9
4.74-4.885.20.2249870.9510.090.2430.75393.6
4.88-5.045.70.22410110.9420.0860.2420.75295.1
5.04-5.226.70.21410070.9670.0740.2280.80495.5
5.22-5.436.80.21610420.950.0760.230.77496.7
5.43-5.677.20.20310320.9610.070.2150.79795.6
5.67-5.977.50.19110280.9780.0640.2020.88595.7
5.97-6.357.90.17310340.9820.0570.1831.03595.9
6.35-6.848.60.14710690.9870.0460.1551.37497.3
6.84-7.528.50.12710680.9910.0410.1341.89997.4
7.52-8.611.30.10411080.9960.0290.1082.32797.7
8.6-10.8212.70.0811250.9980.0220.0832.9698.8
10.82-5011.50.06412370.9980.0190.0672.31997.6

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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: 4→49.877 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1988 9.71 %
Rwork0.2322 18482 -
obs0.2366 20470 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 303.45 Å2 / Biso mean: 152.4158 Å2 / Biso min: 60.02 Å2
Refinement stepCycle: final / Resolution: 4→49.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8088 0 45 2 8135
Biso mean--123.39 64.12 -
Num. residues----1002
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4-4.10.34011350.3076125594
4.1-4.21080.37391330.2959123492
4.2108-4.33460.3271350.2884126594
4.3346-4.47450.34911370.2785126894
4.4745-4.63430.28991360.2581126694
4.6343-4.81970.32451370.2446127093
4.8197-5.03880.26371390.2487129995
5.0388-5.30420.29761400.2341130396
5.3042-5.63610.29331430.2473132197
5.6361-6.07060.31451420.2374131396
6.0706-6.68020.29641440.247134697
6.6802-7.64390.25891490.2159138997
7.6439-9.61920.22211510.1826140298
9.6192-49.8770.23451670.2012155199

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