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

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Basic information

Entry
Database: PDB / ID: 6lpf
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 / 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 / cellular response to L-leucine / tRNA aminoacylation for protein translation / aminoacyl-tRNA editing activity / aminoacyl-tRNA synthetase multienzyme complex / 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 / positive regulation of GTPase activity / cellular response to amino acid stimulus / lysosome / nuclear body / endoplasmic reticulum / ATP binding / cytoplasm / cytosol
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
5'-O-(L-leucylsulfamoyl)adenosine / 2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE / Leucine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 10, 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)251,7546
Polymers250,3772
Non-polymers1,3764
Water12,286682
1
A: Leucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,6482
Polymers125,1891
Non-polymers4591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area43630 Å2
MethodPISA
2
B: Leucine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1064
Polymers125,1891
Non-polymers9173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-1 kcal/mol
Surface area42750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.217, 94.684, 680.055
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1231-

HOH

21B-1255-

HOH

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-VRT / 2'-(L-NORVALYL)AMINO-2'-DEOXYADENOSINE


Mass: 365.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.84 Å3/Da / Density % sol: 56.63 %
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: 97 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 100132 / % possible obs: 99.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.094 / Χ2: 0.996 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.20.70447720.7230.2970.7670.98198.6
2.54-2.597.30.6849980.7930.2650.7320.95299.9
2.59-2.648.30.64249060.8410.2330.6840.96599.9
2.64-2.699.10.5649990.8970.1940.5930.958100
2.69-2.759.40.4849060.9220.1630.5080.966100
2.75-2.8290.40450240.9340.1410.4290.986100
2.82-2.8910.10.35648940.9590.1160.3750.978100
2.89-2.9610.40.31550590.9680.1010.3310.998100
2.96-3.0510.50.25649190.9790.0820.2691.028100
3.05-3.1510.30.21449460.9850.0690.2251.039100
3.15-3.2610.10.17550290.9880.0570.1851.003100
3.26-3.399.70.14149970.9910.0470.1481.044100
3.39-3.559.50.10849660.9930.0370.1141.071100
3.55-3.7310.40.09249790.9970.030.0971.08699.9
3.73-3.9710.30.07550200.9970.0240.0791.084100
3.97-4.2710.20.06350620.9970.0210.0661.122100
4.27-4.79.40.05250570.9980.0180.0551.039100
4.7-5.3810.40.0550890.9980.0160.0520.921100
5.38-6.789.60.04551320.9980.0150.0480.772100
6.78-509.40.03553780.9970.0120.0370.88599.9

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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

1wz2


Resolution: 2.49→49.077 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.2421 4888 5 %
Rwork0.1985 --
obs0.2007 97695 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 49.4063 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 2.49→49.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16212 0 94 682 16988
Biso mean--32.8 36.38 -
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 (%)
2.4902-2.51850.34761010.2795186961
2.5185-2.54810.35141400.283242879
2.5481-2.57920.34241480.2682282588
2.5792-2.61180.29841860.2541294895
2.6118-2.64620.28881630.246305799
2.6462-2.68240.28331930.23733142100
2.6824-2.72070.25641520.23243107100
2.7207-2.76140.2731620.22763161100
2.7614-2.80450.26091660.2337316399
2.8045-2.85050.25171650.23193101100
2.8505-2.89960.28721470.22963141100
2.8996-2.95230.26121540.23583259100
2.9523-3.00910.30731460.23333073100
3.0091-3.07050.27631620.233226100
3.0705-3.13730.29391580.22733125100
3.1373-3.21030.27091760.22493179100
3.2103-3.29050.25981540.22793141100
3.2905-3.37950.27181690.21333237100
3.3795-3.47890.26251640.20883104100
3.4789-3.59110.24681970.20783201100
3.5911-3.71940.26081570.23141100
3.7194-3.86830.25041620.18373180100
3.8683-4.04430.1971700.17823249100
4.0443-4.25740.19991680.173165100
4.2574-4.5240.19861380.15853232100
4.524-4.8730.19141610.15773209100
4.873-5.36280.21841770.16993238100
5.3628-6.13760.22371860.18253198100
6.1376-7.72780.22911680.17953295100
7.7278-49.0770.18011980.1513341399

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