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- PDB-8tc8: Human asparaginyl-tRNA synthetase bound to adenosine 5'-sulfamate -

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Basic information

Entry
Database: PDB / ID: 8tc8
TitleHuman asparaginyl-tRNA synthetase bound to adenosine 5'-sulfamate
ComponentsAsparagine--tRNA ligase, cytoplasmic
KeywordsLIGASE / enzyme / synthase / drug target
Function / homology
Function and homology information


CCR3 chemokine receptor binding / asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity ...CCR3 chemokine receptor binding / asparagine-tRNA ligase / asparagine-tRNA ligase activity / asparaginyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / cerebral cortex development / cell migration / nucleic acid binding / protein dimerization activity / extracellular exosome / ATP binding / cytoplasm / cytosol
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
5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / 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)255,51828
Polymers252,1074
Non-polymers3,41124
Water28,6261589
1
A: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,75914
Polymers126,0542
Non-polymers1,70612
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)127,75914
Polymers126,0542
Non-polymers1,70612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.851, 126.285, 160.598
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 214 or resid 223 through 548 or resid 601 through 603))
d_2ens_1(chain "B" and (resid 110 through 214 or resid 223 through 548 or resid 601 through 603))
d_3ens_1(chain "C" and (resid 110 through 214 or resid 223 through 548 or resid 601 through 603))
d_4ens_1(chain "D" and (resid 110 through 214 or resid 223 through 548 or resid 601 through 603))

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_11PROPROGLYGLYAA110 - 214110 - 214
d_12GLUGLUPROPROAA223 - 548223 - 548
d_13NSSNSSNSSNSSAE601
d_14GOLGOLGOLGOLAF602
d_15GOLGOLGOLGOLAG603
d_21PROPROGLYGLYBB110 - 214110 - 214
d_22GLUGLUPROPROBB223 - 548223 - 548
d_23NSSNSSNSSNSSBM601
d_24GOLGOLGOLGOLBN602
d_25GOLGOLGOLGOLBO603
d_31PROPROGLYGLYCC110 - 214110 - 214
d_32GLUGLUPROPROCC223 - 434223 - 434
d_33NSSNSSNSSNSSCU601
d_34GOLGOLGOLGOLCV602
d_35GOLGOLGOLGOLCW603
d_41PROPROGLYGLYDD110 - 214110 - 214
d_42GLUGLUPROPRODD223 - 434223 - 434
d_43NSSNSSNSSNSSDY601
d_44GOLGOLGOLGOLDZ602
d_45GOLGOLGOLGOLDAA603

NCS oper:
IDCodeMatrixVector
1given(-0.999809413845, 0.013376288626, -0.0142200875217), (-0.0134260788347, -0.999904045698, 0.00341171573874), (-0.0141730869487, 0.00360198552906, 0.999893068936)-0.238227189464, -0.383938168108, 43.4742928478
2given(-0.778429001065, 0.627731443766, 0.00123483138281), (0.627718589048, 0.77842321845, -0.00516390761056), (-0.0042027685991, -0.00324460882955, -0.999985904525)6.47875338492, 18.1655106902, 28.961519037
3given(0.773470376235, -0.633679154518, 0.0139393764814), (-0.633697712442, -0.773572363713, -0.00360656984196), (0.0130685245415, -0.00604377605654, -0.999896337846)-6.53756125406, -18.4690391842, -14.4324807135

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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-NSS / 5'-O-[N-(L-ASPARAGINYL)SULFAMOYL]ADENOSINE / ASN-SA


Mass: 461.430 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H21N8O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1589 / 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: 47.21 %
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→49.29 Å / Num. obs: 185028 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.072 / Rrim(I) all: 0.192 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 2.601 / Num. unique obs: 9037 / CC1/2: 0.502 / Rpim(I) all: 1.186 / Rrim(I) all: 3.07

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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: 1.9→49.29 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5184
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 9326 5.05 %
Rwork0.1809 175214 -
obs0.1827 184540 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14007 0 224 1589 15820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007514559
X-RAY DIFFRACTIONf_angle_d0.860119698
X-RAY DIFFRACTIONf_chiral_restr0.0512086
X-RAY DIFFRACTIONf_plane_restr0.00862557
X-RAY DIFFRACTIONf_dihedral_angle_d12.86315451
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.37652462805
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS2.79211964622
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS2.79935232246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.38652970.3735653X-RAY DIFFRACTION97.32
1.92-1.940.37963010.33395822X-RAY DIFFRACTION99.56
1.94-1.970.35623160.32535759X-RAY DIFFRACTION99.69
1.97-1.990.36052920.30575798X-RAY DIFFRACTION99.67
1.99-2.020.33553200.29625753X-RAY DIFFRACTION99.79
2.02-2.050.34743270.28835801X-RAY DIFFRACTION99.82
2.05-2.080.30442860.26485792X-RAY DIFFRACTION99.56
2.08-2.110.29792980.25995820X-RAY DIFFRACTION99.69
2.11-2.140.29073040.24615800X-RAY DIFFRACTION99.77
2.14-2.170.27263030.23465824X-RAY DIFFRACTION99.79
2.17-2.210.26183320.22365747X-RAY DIFFRACTION99.74
2.21-2.250.28452890.22615843X-RAY DIFFRACTION99.84
2.25-2.30.2763080.21025819X-RAY DIFFRACTION99.85
2.3-2.340.26093030.20695808X-RAY DIFFRACTION99.9
2.34-2.390.24162970.20115843X-RAY DIFFRACTION99.87
2.39-2.450.23333380.18525799X-RAY DIFFRACTION99.89
2.45-2.510.22263090.18485835X-RAY DIFFRACTION99.97
2.51-2.580.23673030.18055844X-RAY DIFFRACTION99.85
2.58-2.650.21373250.17545798X-RAY DIFFRACTION99.77
2.65-2.740.21743390.17525827X-RAY DIFFRACTION99.87
2.74-2.840.23253040.17165855X-RAY DIFFRACTION99.84
2.84-2.950.20493310.16575809X-RAY DIFFRACTION99.74
2.95-3.090.19833340.16565864X-RAY DIFFRACTION99.9
3.09-3.250.19133070.16255881X-RAY DIFFRACTION99.81
3.25-3.450.18923240.15595842X-RAY DIFFRACTION99.76
3.45-3.720.16983020.14275924X-RAY DIFFRACTION99.84
3.72-4.090.17383230.13965901X-RAY DIFFRACTION99.92
4.09-4.680.15673080.12285956X-RAY DIFFRACTION99.87
4.68-5.90.16672990.1486018X-RAY DIFFRACTION99.78
5.9-49.290.18673070.16696179X-RAY DIFFRACTION98.9
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)
10.2675948975960.03246297018310.1650809018490.3256764708220.1771913483431.15519985387-0.001773442105410.02533189512080.021149408614-0.0180703589169-0.0177746952494-0.0206098244839-0.2108488047360.006540019345360.01820880186290.1991552382310.0200274923601-0.01652537958620.2532380790550.008339468677440.255356502943-20.49526798339.40720706159-11.0484689765
20.3565646804580.0856069343382-0.05760874414340.488695332985-0.1421253241491.040184078950.001520176551760.0285592601193-0.0172405177905-0.0098830203675-0.009109654886940.01022732854760.04905925367760.02882787736930.0007243427684040.1521510128810.0226076805737-0.0002246529489040.196564193919-0.002811833376070.20951114223220.4848195993-9.5244980821332.8927075448
30.390583698902-0.0364888725808-0.01516297593660.446851802579-0.1147463013491.597212035450.0354076586346-0.08500510018690.1138197296420.02088746091410.0130111634158-0.0152596738163-0.5068793310980.0780811467288-0.06441837767560.29543544215-0.0268014983913-0.0003307217311980.211556206691-0.02153834253740.24623461561328.280141324312.679963402240.0788040497
40.377302186544-0.05008471973030.3662132496030.2757146531010.002240511783341.706372853860.0450383329215-0.0506881133759-0.0626319307579-0.03258863870380.00170113952010.0303814929350.412229096405-0.257110513791-0.04562845137440.248847439796-0.0421097189719-0.01015022569420.2291147317930.009615068557820.250420135215-28.4675156756-12.7084172091-3.68432812579
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 110 through 548)AA110 - 5481 - 435
22(chain 'B' and resid 109 through 548)BI109 - 5481 - 433
33(chain 'C' and resid 109 through 548)CQ109 - 5481 - 434
44(chain 'D' and resid 109 through 548)DU109 - 5481 - 434

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