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- PDB-8tc9: Human asparaginyl-tRNA synthetase bound to OSM-S-106 -

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Basic information

Entry
Database: PDB / ID: 8tc9
TitleHuman asparaginyl-tRNA synthetase bound to OSM-S-106
ComponentsAsparagine--tRNA ligase, cytoplasmic
KeywordsLIGASE / enzyme / synthase / drug target
Function / homology
Function and homology information


asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / CCR3 chemokine receptor binding / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity ...asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / CCR3 chemokine receptor binding / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
: / Asparaginal-tRNA synthetase, N-terminal domain / Asparagine-tRNA ligase / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...: / Asparaginal-tRNA synthetase, N-terminal domain / Asparagine-tRNA ligase / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Asparagine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDogovski, C. / Metcalfe, R.D. / Xie, S.C. / Morton, C.J. / Tilley, L. / Griffin, M.D.W.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1171794 Australia
CitationJournal: Nat Commun / Year: 2024
Title: Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase.
Authors: Xie, S.C. / Wang, Y. / Morton, C.J. / Metcalfe, R.D. / Dogovski, C. / Pasaje, C.F.A. / Dunn, E. / Luth, M.R. / Kumpornsin, K. / Istvan, E.S. / Park, J.S. / Fairhurst, K.J. / Ketprasit, N. / ...Authors: Xie, S.C. / Wang, Y. / Morton, C.J. / Metcalfe, R.D. / Dogovski, C. / Pasaje, C.F.A. / Dunn, E. / Luth, M.R. / Kumpornsin, K. / Istvan, E.S. / Park, J.S. / Fairhurst, K.J. / Ketprasit, N. / Yeo, T. / Yildirim, O. / Bhebhe, M.N. / Klug, D.M. / Rutledge, P.J. / Godoy, L.C. / Dey, S. / De Souza, M.L. / Siqueira-Neto, J.L. / Du, Y. / Puhalovich, T. / Amini, M. / Shami, G. / Loesbanluechai, D. / Nie, S. / Williamson, N. / Jana, G.P. / Maity, B.C. / Thomson, P. / Foley, T. / Tan, D.S. / Niles, J.C. / Han, B.W. / Goldberg, D.E. / Burrows, J. / Fidock, D.A. / Lee, M.C.S. / Winzeler, E.A. / Griffin, M.D.W. / Todd, M.H. / Tilley, L.
History
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asparagine--tRNA ligase, cytoplasmic
B: Asparagine--tRNA ligase, cytoplasmic
C: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,38147
Polymers252,1074
Non-polymers5,27443
Water18,5731031
1
A: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,64423
Polymers126,0542
Non-polymers2,59121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Asparagine--tRNA ligase, cytoplasmic
C: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,73624
Polymers126,0542
Non-polymers2,68322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.088, 126.810, 161.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 110 through 213 or resid 220...
d_2ens_1(chain "B" and (resid 110 through 374 or resid 376...
d_3ens_1(chain "C" and (resid 110 through 374 or resid 376...
d_4ens_1(chain "D" and (resid 110 through 213 or resid 220...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROALAALAAA110 - 213110 - 213
d_12ILEILEVALVALAA220 - 374220 - 374
d_13GLUGLUTYRTYRAA376 - 531376 - 531
d_14ILEILEPROPROAA419 - 434419 - 434
d_15ZTEZTEZTEZTEAE601
d_16GOLGOLGOLGOLAF602
d_17GOLGOLGOLGOLAG603
d_18GOLGOLGOLGOLAH604
d_19GOLGOLGOLGOLAI605
d_110GOLGOLGOLGOLAJ606
d_111GOLGOLGOLGOLAK607
d_112GOLGOLGOLGOLAL608
d_21PROPROVALVALBB110 - 374110 - 374
d_22GLUGLUTYRTYRBB376 - 531376 - 531
d_23ILEILEPROPROBB419 - 434419 - 434
d_24ZTEZTEZTEZTEBN601
d_25GOLGOLGOLGOLBO602
d_26GOLGOLGOLGOLBP603
d_27GOLGOLGOLGOLBQ604
d_31PROPROVALVALCC110 - 374110 - 374
d_32GLUGLUTYRTYRCC376 - 531376 - 531
d_33ILEILEPROPROCC533 - 548533 - 548
d_34ZTEZTEZTEZTECBA602
d_35GOLGOLGOLGOLCAA601
d_36GOLGOLGOLGOLCCA603
d_37GOLGOLGOLGOLCDA604
d_38GOLGOLGOLGOLCEA605
d_39GOLGOLGOLGOLCFA606
d_310GOLGOLGOLGOLCGA607
d_311GOLGOLGOLGOLCHA608
d_41PROPROALAALADD110 - 213110 - 213
d_42ILEILEVALVALDD220 - 374220 - 374
d_43GLUGLUTYRTYRDD376 - 531376 - 531
d_44ILEILEPROPRODD419 - 434419 - 434
d_45ZTEZTEZTEZTEDJA601
d_46GOLGOLGOLGOLDKA602
d_47GOLGOLGOLGOLDLA603
d_48GOLGOLGOLGOLDMA604
d_49GOLGOLGOLGOLDNA605
d_410GOLGOLGOLGOLDOA606
d_411GOLGOLGOLGOLDPA607
d_412GOLGOLGOLGOLDQA608

NCS oper:
IDCodeMatrixVector
1given(-0.999758510337, 0.0120086109624, -0.0184041916886), (-0.0122026178928, -0.99987077473, 0.010465656062), (-0.0182761354099, 0.0106877080331, 0.999775852765)-0.304330111749, -0.309542244804, 43.1606868576
2given(-0.775672952121, 0.631028401968, 0.01160289865), (0.631034570084, 0.77574643219, -0.00358389498758), (-0.0112624467577, 0.00454189975625, -0.999926261501)6.49454900368, 18.1726719764, 29.0277297788
3given(0.776508835662, -0.630088459358, 0.00474989719225), (-0.630095123642, -0.776517946335, -0.000119087719977), (0.00376341621104, -0.00290041439185, -0.999988712084)-6.65470576931, -18.2011453116, -14.2442056094

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Components

#1: Protein
Asparagine--tRNA ligase, cytoplasmic / Asparaginyl-tRNA synthetase / AsnRS / Asparaginyl-tRNA synthetase 1


Mass: 63026.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NARS1, NARS, NRS / Production host: Escherichia coli (E. coli) / References: UniProt: O43776, asparagine-tRNA ligase
#2: Chemical
ChemComp-ZTE / N~1~-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-aspartamide


Mass: 420.466 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H16N6O4S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 39 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) glycerol, 40 mM potassium phosphate and 14% polyethylene glycol 8,000, and 100-mM Tris pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→49.46 Å / Num. obs: 159099 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 30.63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.111 / Rrim(I) all: 0.212 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 2.306 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7783 / CC1/2: 0.471 / Rpim(I) all: 1.419 / Rrim(I) all: 2.718

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIX

5xix


Resolution: 2→49.46 Å / SU ML: 0.2612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2207 7948 5.01 %
Rwork0.1816 150816 -
obs0.1835 158764 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.33 Å2
Refinement stepCycle: LAST / Resolution: 2→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14016 0 346 1031 15393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006914743
X-RAY DIFFRACTIONf_angle_d0.872419913
X-RAY DIFFRACTIONf_chiral_restr0.05052080
X-RAY DIFFRACTIONf_plane_restr0.00872578
X-RAY DIFFRACTIONf_dihedral_angle_d13.66255531
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.44431056673
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS3.85501814162
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS4.13769924852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.35812370.34394953X-RAY DIFFRACTION98.74
2.02-2.050.35022870.30914970X-RAY DIFFRACTION99.87
2.05-2.070.30092540.2934963X-RAY DIFFRACTION99.79
2.07-2.10.33992620.28464981X-RAY DIFFRACTION99.77
2.1-2.130.28652590.27044981X-RAY DIFFRACTION99.83
2.13-2.150.31492810.26834975X-RAY DIFFRACTION99.87
2.15-2.190.27142640.25584978X-RAY DIFFRACTION99.87
2.19-2.220.29332550.24354993X-RAY DIFFRACTION99.68
2.22-2.250.29582770.24624993X-RAY DIFFRACTION99.83
2.25-2.290.26882420.23034964X-RAY DIFFRACTION99.9
2.29-2.330.26932530.22375030X-RAY DIFFRACTION99.87
2.33-2.370.2622710.21684986X-RAY DIFFRACTION99.92
2.37-2.420.24762360.20235030X-RAY DIFFRACTION99.79
2.42-2.470.23952660.19994988X-RAY DIFFRACTION99.9
2.47-2.520.27972520.20585034X-RAY DIFFRACTION99.94
2.52-2.580.25482680.19394990X-RAY DIFFRACTION99.83
2.58-2.640.242770.18825038X-RAY DIFFRACTION99.92
2.64-2.710.25822800.18424961X-RAY DIFFRACTION99.89
2.71-2.790.23962750.17815020X-RAY DIFFRACTION99.89
2.79-2.880.24852160.18865083X-RAY DIFFRACTION99.89
2.88-2.990.24892660.18415004X-RAY DIFFRACTION99.85
2.99-3.110.22422930.18365035X-RAY DIFFRACTION99.83
3.11-3.250.2372840.17655013X-RAY DIFFRACTION99.74
3.25-3.420.22732840.17095026X-RAY DIFFRACTION99.81
3.42-3.630.19352560.15735050X-RAY DIFFRACTION99.81
3.63-3.910.18262620.14785095X-RAY DIFFRACTION99.98
3.91-4.310.15752750.13145081X-RAY DIFFRACTION99.89
4.31-4.930.14762820.1245095X-RAY DIFFRACTION99.76
4.93-6.210.18852430.15625200X-RAY DIFFRACTION99.74
6.21-49.460.18062910.16275306X-RAY DIFFRACTION98.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.270352048475-0.01801014509770.1190860944870.2552764919330.1204705298481.156425507220.00796258417730.03190463885720.0318066280936-0.0362242393776-0.0203986450119-0.02263535026-0.250236069107-0.04980853524140.000127382154650.1994882019820.00386452554833-0.007037571486720.2116654628650.00840334443140.273436450351-20.4579.428-10.986
20.4371388835910.150104521165-0.01564602853980.558121929337-0.06951285233631.09715362277-0.0180370572230.0295452626374-0.01540504720780.00540583375541-0.009426159470110.005310716169-0.03722578133860.0144562335190.02143050791680.1841243074810.01288078084360.003405048918870.187489115123-0.01226718791380.24615834122720.423-9.59332.708
30.5839960077570.0984803758012-0.110781859620.451161434787-0.09880583184161.811240829220.0212346491801-0.08754274084080.1645895658550.0609284511909-0.01303366020720.00687392265157-0.7316899791440.1889079555-0.05993087901480.501465810407-0.0711192699411-0.01542568016540.237947401143-0.02207493195050.32435773168228.17312.78740.16
40.50439013257-0.06444383441930.4492970720950.2075013445330.002281117340522.020434919370.0598840813531-0.0392085580005-0.093851976497-0.04612299745450.003437794253180.01514364820620.508377325218-0.326774267001-0.05154134876640.285240398135-0.0784738718851-0.006110347801760.219193678960.009775809391170.284794885912-28.543-12.822-3.525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 110:548 )A110 - 548
2X-RAY DIFFRACTION2( CHAIN B AND RESID 109:548 )B109 - 548
3X-RAY DIFFRACTION3( CHAIN C AND RESID 110:548 )C110 - 548
4X-RAY DIFFRACTION4( CHAIN D AND RESID 110:548 )D110 - 548

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