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- PDB-6lr6: The crystal structure of human cytoplasmic LRS -

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Basic information

Entry
Database: PDB / ID: 6lr6
TitleThe crystal structure of human cytoplasmic LRS
ComponentsLeucine--tRNA ligase, cytoplasmic
KeywordsRNA BINDING PROTEIN / tRNA / aminoacylation / protein translation / LeuRS
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 / cellular response to L-leucine / aminoacyl-tRNA synthetase multienzyme complex ...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 / cellular response to L-leucine / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / regulation of cell size / positive regulation of TOR signaling / endomembrane system / positive regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / cellular response to amino acid stimulus / positive regulation of GTPase activity / lysosome / nuclear body / endoplasmic reticulum / ATP binding / cytosol / cytoplasm
Similarity search - Function
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
Chem-A2H / 5'-O-(L-leucylsulfamoyl)adenosine / Leucine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.009 Å
AuthorsLiu, R.J. / Long, T. / Li, H. / Li, J. / Zhao, J.H. / Lin, J.Z. / Palencia, A. / Wang, M.Z. / Cusack, S. / Wang, E.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770842 China
National Natural Science Foundation of China (NSFC)31971230 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Molecular basis of the multifaceted functions of human leucyl-tRNA synthetase in protein synthesis and beyond.
Authors: Liu, R.J. / Long, T. / Li, H. / Zhao, J. / Li, J. / Wang, M. / Palencia, A. / Lin, J. / Cusack, S. / Wang, E.D.
History
DepositionJan 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)252,4326
Polymers250,3772
Non-polymers2,0544
Water18010
1
A: Leucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2163
Polymers125,1891
Non-polymers1,0272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,2163
Polymers125,1891
Non-polymers1,0272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.854, 95.798, 682.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 125188.727 Da / Num. of mol.: 2
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-LSS / 5'-O-(L-leucylsulfamoyl)adenosine / 5-O-N-LEUCYL-SULFAMOYLADENOSINE


Mass: 459.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O7S
#3: Chemical ChemComp-A2H / 4-Chloro-3-aminomethyl-7-[ethoxy]-3H-benzo[C][1,2]oxaborol-1-ol modified adenosine


Mass: 567.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22BClN6O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 20% (w/v) PEG 6000, 100 mM Tris-Cl, pH 8.0, and 200 mM Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45642 / % possible obs: 77.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.06 / Rrim(I) all: 0.131 / Χ2: 0.884 / Net I/σ(I): 6.4 / Num. measured all: 185795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.90.53943050.7570.2770.610.91274.2
3.11-3.234.10.41844400.8190.2150.4720.94177.4
3.23-3.3840.30144880.8920.1580.3410.90477.4
3.38-3.564.30.21845570.9350.1070.2440.89578.4
3.56-3.784.20.1645530.9680.0790.1790.87978.3
3.78-4.073.90.1345940.9680.0660.1460.88177.9
4.07-4.484.20.10544910.9810.0520.1180.83177.4
4.48-5.134.20.08945020.9860.0440.10.71176.5
5.13-6.464.10.07446420.9880.0370.0830.5177.4
6.46-503.90.09350700.8530.0510.1071.37481.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZ2, 2WFD

1wz2

2wfd


Resolution: 3.009→49.412 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2602 2242 5.12 %
Rwork0.2109 --
obs0.2135 43749 74.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.13 Å2 / Biso mean: 59.2115 Å2 / Biso min: 7.19 Å2
Refinement stepCycle: final / Resolution: 3.009→49.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16210 0 138 10 16358
Biso mean--57.36 20.9 -
Num. residues----2008
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.009-3.0740.3411040.2987173051
3.074-3.14550.38161170.2839219665
3.1455-3.22420.34471090.2793244971
3.2242-3.31130.36491370.2756254474
3.3113-3.40870.34531570.27264777
3.4087-3.51870.2981340.2342264178
3.5187-3.64450.25471540.2246268977
3.6445-3.79030.26911360.2188267678
3.7903-3.96280.28651490.2177269678
3.9628-4.17160.24551500.208268577
4.1716-4.43280.23921410.1924268277
4.4328-4.77480.22611720.1789259276
4.7748-5.25480.24211400.1838270477
5.2548-6.01410.251300.1951276377
6.0141-7.57270.23931600.191279179
7.5727-49.4120.1931520.1761302281

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