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- PDB-8tc7: Human asparaginyl-tRNA synthetase, apo form -

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Basic information

Entry
Database: PDB / ID: 8tc7
TitleHuman asparaginyl-tRNA synthetase, apo form
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: 1.9 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)209,67028
Polymers207,5734
Non-polymers2,09724
Water19,9071105
1
A: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,70712
Polymers103,7862
Non-polymers92110
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)104,96216
Polymers103,7862
Non-polymers1,17614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.490, 127.195, 163.160
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 109 through 447 or resid 449...
d_2ens_1(chain "B" and (resid 109 through 213 or resid 219...
d_3ens_1(chain "C" and (resid 109 through 277 or resid 282...
d_4ens_1(chain "D" and (resid 109 through 277 or resid 282...

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_11LEULEUPHEPHEAA109 - 44714 - 352
d_12METMETGLNGLNAA449 - 450354 - 355
d_13CYSCYSPROPROAA452 - 548357 - 453
d_14GOLGOLGOLGOLAE601
d_15GOLGOLGOLGOLAF602
d_16GOLGOLGOLGOLAG603
d_21LEULEUALAALABB109 - 21314 - 118
d_22LEULEUGLNGLNBB219 - 277124 - 182
d_23ALAALAGLUGLUBB282 - 324187 - 229
d_24ARGARGPHEPHEBB330 - 447235 - 352
d_25METMETGLNGLNBB449 - 450354 - 355
d_26CYSCYSPROPROBB452 - 548357 - 453
d_27GOLGOLGOLGOLBL601
d_28GOLGOLGOLGOLBM602
d_29GOLGOLGOLGOLBN603
d_31LEULEUGLNGLNCC109 - 27714 - 182
d_32ALAALAPHEPHECC282 - 447187 - 352
d_33METMETGLNGLNCC449 - 450354 - 355
d_34CYSCYSPROPROCC452 - 548357 - 453
d_35GOLGOLGOLGOLCV601
d_36GOLGOLGOLGOLCW602
d_37GOLGOLGOLGOLCX603
d_41LEULEUGLNGLNDD109 - 27714 - 182
d_42ALAALAGLUGLUDD282 - 324187 - 229
d_43ARGARGPHEPHEDD330 - 447235 - 352
d_44METMETGLNGLNDD449 - 450354 - 355
d_45CYSCYSPROPRODD452 - 548357 - 453
d_46GOLGOLGOLGOLDZ601
d_47GOLGOLGOLGOLAK607
d_48GOLGOLGOLGOLDAA602

NCS oper:
IDCodeMatrixVector
1given(-0.999897347991, 0.00711937732144, 0.0124341444365), (-0.0069789656048, -0.999911803234, 0.011299548284), (0.012513493533, 0.0112116108963, 0.999858846168)-0.705598396367, -0.410034048099, 39.3631111098
2given(-0.770716197888, 0.635115165527, -0.0512373772801), (0.635471251541, 0.772044595636, 0.0111099421193), (0.0466136329517, -0.0239972679169, -0.998624704459)5.64030941793, 18.576221468, 30.4247992034
3given(0.764517625577, -0.644237306812, 0.0217046698576), (-0.643966470918, -0.764825600709, -0.0186811357633), (0.0286353717544, 0.000304977906207, -0.999589877136)-6.65448052738, -18.9574289661, -9.49023084247

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Components

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


Mass: 51893.227 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 56.64 %
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: 1.9→49.05 Å / Num. obs: 185343 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 28.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.117 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 2.021 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 8986 / CC1/2: 0.513 / Rpim(I) all: 1.253 / Rrim(I) all: 2.386

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.58 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 26.6156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 9062 4.9 %
Rwork0.1805 175928 -
obs0.1823 184990 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.91 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13838 0 134 1105 15077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314332
X-RAY DIFFRACTIONf_angle_d1.171619367
X-RAY DIFFRACTIONf_chiral_restr0.0712057
X-RAY DIFFRACTIONf_plane_restr0.01212514
X-RAY DIFFRACTIONf_dihedral_angle_d12.47655397
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS4.76010071366
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS4.13851872669
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS4.66386435712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.42382830.39615707X-RAY DIFFRACTION98.1
1.92-1.940.39972840.35115793X-RAY DIFFRACTION99.85
1.94-1.970.35183060.34075866X-RAY DIFFRACTION99.94
1.97-1.990.36443240.31365761X-RAY DIFFRACTION99.82
1.99-2.020.33472810.30055863X-RAY DIFFRACTION99.77
2.02-2.050.32882730.2735827X-RAY DIFFRACTION99.97
2.05-2.080.31253040.26775807X-RAY DIFFRACTION99.77
2.08-2.110.30242960.23975832X-RAY DIFFRACTION99.55
2.11-2.140.25283110.22435806X-RAY DIFFRACTION99.84
2.14-2.170.28413120.21725818X-RAY DIFFRACTION99.71
2.17-2.210.26532900.21695825X-RAY DIFFRACTION99.69
2.21-2.250.25573180.20285787X-RAY DIFFRACTION99.54
2.25-2.30.24822970.19495844X-RAY DIFFRACTION99.8
2.3-2.340.24833080.19275845X-RAY DIFFRACTION99.79
2.34-2.390.22892990.19015828X-RAY DIFFRACTION99.89
2.39-2.450.2252910.18695854X-RAY DIFFRACTION99.79
2.45-2.510.26692950.18495865X-RAY DIFFRACTION99.81
2.51-2.580.23832990.17835863X-RAY DIFFRACTION99.68
2.58-2.650.22053170.17175846X-RAY DIFFRACTION99.79
2.65-2.740.23153020.17135847X-RAY DIFFRACTION99.77
2.74-2.840.23222960.17595891X-RAY DIFFRACTION99.73
2.84-2.950.2312820.17895866X-RAY DIFFRACTION99.77
2.95-3.090.23233140.18445864X-RAY DIFFRACTION99.94
3.09-3.250.21813250.175876X-RAY DIFFRACTION99.76
3.25-3.450.19092910.16435921X-RAY DIFFRACTION99.89
3.45-3.720.20333040.16285926X-RAY DIFFRACTION99.92
3.72-4.090.17213130.13835941X-RAY DIFFRACTION99.87
4.09-4.680.13383100.12165960X-RAY DIFFRACTION99.84
4.68-5.90.16233140.14536025X-RAY DIFFRACTION99.73
5.9-46.580.19333230.16856174X-RAY DIFFRACTION98.87
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)
10.3169742572380.05933628855410.2909125446820.6863294078910.1818566758441.640772150020.001987763589990.09978404070980.040973228765-0.0483900161026-0.0329912949897-0.0303533517779-0.1569882302450.1292113984420.01956864251560.2485408382750.0401412447628-0.0146826031880.2453765067590.01432441887330.21356608777-21.1399579079.52132126575-8.09149631422
20.307804237044-0.0162166053580.09431834320430.601945080556-0.04502700638121.2591579814-0.0151270829042-0.00308196961588-0.02187689604260.043450141141-0.05143860216020.008935313774640.1600127718560.03269586642170.0613092912530.2700347298990.05233315702740.01588028935340.1980308306280.005425821267350.22189543858520.4621366573-9.8742803943131.0644972369
30.3543284749620.10622754990.1804275609710.47765231972-0.3538123620482.15993792018-0.025910398245-0.04477226416470.1185499547090.0602628689391-0.0366778445195-0.0357262806487-0.6575895662030.131827846291-0.01123731220220.4281471555730.0107525466904-0.0276618470720.2314235233140.007666329454310.2787784077828.428030234812.382609081537.3770799392
40.5092325754370.06192788757490.2994862715430.408313097720.159847918782.06981371360.0855070443284-0.0204540461971-0.1211184501130.00120252587587-0.02888000893040.04004797275540.555013812081-0.179726798723-0.06843294019610.393758373803-0.0109708376927-0.0198689230610.220344900466-0.005096355608970.25450040083-29.1612316712-12.4755560441-1.80493737474
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 109 - 548

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDLabel seq-ID
11(chain 'A' and resid 109 through 548)AA1 - 426
22(chain 'B' and resid 109 through 548)BH1 - 429
33(chain 'C' and resid 109 through 548)CR1 - 428
44(chain 'D' and resid 109 through 548)DV1 - 428

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