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- PDB-8h53: Human asparaginyl-tRNA synthetase in complex with asparagine-AMP -

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Basic information

Entry
Database: PDB / ID: 8h53
TitleHuman asparaginyl-tRNA synthetase in complex with asparagine-AMP
ComponentsAsparagine--tRNA ligase, cytoplasmic
KeywordsRNA BINDING PROTEIN / asparagine / complex / synthetase / tRNA
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
IMIDODIPHOSPHORIC ACID / Chem-4AD / Asparagine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPark, J.S. / Han, B.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
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
DepositionOct 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)221,17646
Polymers216,0304
Non-polymers5,14642
Water13,439746
1
A: Asparagine--tRNA ligase, cytoplasmic
D: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,68024
Polymers108,0152
Non-polymers2,66522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13590 Å2
ΔGint-94 kcal/mol
Surface area31290 Å2
MethodPISA
2
B: Asparagine--tRNA ligase, cytoplasmic
C: Asparagine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,49622
Polymers108,0152
Non-polymers2,48120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13300 Å2
ΔGint-95 kcal/mol
Surface area31470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.423, 125.842, 161.134
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

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 54007.523 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

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Non-polymers , 5 types, 788 molecules

#2: Chemical
ChemComp-4AD / 4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE / ASNAMP


Mass: 462.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H21N7O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-2PN / IMIDODIPHOSPHORIC ACID


Mass: 176.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H5NO6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 40 mM potassium phosphate, 20% (v/v) glycerol, 16% (w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 126122 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 30.77 Å2 / CC1/2: 0.993 / Net I/σ(I): 12.3
Reflection shellResolution: 2.16→2.2 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6260 / CC1/2: 0.868

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XIX

5xix


Resolution: 2.16→49.88 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2368 6229 4.97 %
Rwork0.2034 119065 -
obs0.205 125294 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.86 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13501 0 324 746 14571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002814129
X-RAY DIFFRACTIONf_angle_d0.572819165
X-RAY DIFFRACTIONf_chiral_restr0.042056
X-RAY DIFFRACTIONf_plane_restr0.00512470
X-RAY DIFFRACTIONf_dihedral_angle_d7.37471992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.20.32133400.27475817X-RAY DIFFRACTION98.4
2.2-2.240.32043060.28155869X-RAY DIFFRACTION99.1
2.24-2.280.29023320.26125856X-RAY DIFFRACTION99.25
2.28-2.330.27693030.25325882X-RAY DIFFRACTION99.26
2.33-2.380.29443370.24835860X-RAY DIFFRACTION99.22
2.38-2.430.27873150.23395876X-RAY DIFFRACTION99.18
2.43-2.490.28773190.23565879X-RAY DIFFRACTION99.42
2.49-2.560.26632920.245947X-RAY DIFFRACTION99.33
2.56-2.640.2843010.21955909X-RAY DIFFRACTION99.42
2.64-2.720.29792850.21915937X-RAY DIFFRACTION99.38
2.72-2.820.25832540.2155994X-RAY DIFFRACTION99.44
2.82-2.930.24863440.21465920X-RAY DIFFRACTION99.48
2.93-3.060.26313350.2145911X-RAY DIFFRACTION99.71
3.06-3.230.24033010.20865977X-RAY DIFFRACTION99.52
3.23-3.430.23413030.19165971X-RAY DIFFRACTION99.57
3.43-3.690.22533310.18545989X-RAY DIFFRACTION99.81
3.69-4.060.22063350.17836005X-RAY DIFFRACTION99.83
4.06-4.650.16972980.15766064X-RAY DIFFRACTION99.87
4.65-5.860.19523160.18276107X-RAY DIFFRACTION99.75
5.86-49.880.19582820.19426295X-RAY DIFFRACTION98.65
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)
10.5090953040420.0712569591905-0.007999393283730.8829561480630.5701313444474.09716342548-0.01600061483510.0680476760337-0.0220265066796-0.07486530593620.0561431266573-0.04925525297050.1289505727280.133836800486-0.04384967987330.165124579828-0.01977497544190.00274331660670.131827839121-0.004286642073970.24976936649238.14520391892.9025397102324.5748695148
20.5703444556270.410525788158-0.1134560272121.3122516136-0.01937915575012.243925365090.05894431026620.03316877492440.1388710676730.0605170901143-0.08216229995890.0933667330923-0.367737235281-0.17502246380.01160673832320.2251167655770.05655132380370.002263800001250.1970426298030.009797312898130.23847656490735.714111352818.691314650445.1587066345
30.4218574462220.0702898576899-0.2391679250350.622985049397-0.4415911361524.051181163550.01384272298990.0677167838589-0.0673833923571-0.0229358767237-0.02035610350340.06598063865360.170984543723-0.123508147504-0.006527220550330.121390968172-0.01139579134130.007903136983350.148735153863-0.02224182446530.25954093839777.1640463314-2.50156562172-19.1295526937
40.5499826787110.230817663215-0.04772308883421.859570225060.1925586888672.207730441590.02420278107660.0770238730488-0.171903963349-0.0725686141656-0.0619495314841-0.04463132114710.5495553456890.1787842041870.02873475836920.2670996953430.06626781524640.03249303381060.213969333481-0.01396243539030.25623467694779.7385383767-18.62140158071.43628034402
55.12114137776-0.00678471486256-0.533624723342.085801632-0.03148190455413.79201280092-0.114509592483-0.2176387789930.3692833351620.1581806267920.1056721233610.0988367572766-0.432005501887-0.0489270462205-0.00064156821890.2241240675290.00178924982670.006319882384740.176556740109-0.03182800610460.20957346504374.76245632567.6635050130124.8309926812
61.14577046099-1.43540063868E-6-0.4357926054381.423536983430.2636498028363.033198605120.0736486556354-0.1093052715240.265512741881-0.0570274322220.0313973968242-0.149797426047-0.7155399986330.426380587913-0.09232166351420.355636009243-0.09435807409130.02534567939630.22979689726-0.00422251198750.27293637720590.268903992914.2113506822-14.5911621461
74.4065487675-0.4001843874360.2214546152883.29221347826-0.7148610992283.181243542590.149914197387-0.338835656096-0.4620803168740.244037820723-0.22264005415-0.503675747930.9842877199470.8791620554010.07905468838910.5892033155370.114725506739-0.09247494846030.4769282860290.08996085710580.36412784785245.2991670031-8.4330852983669.6851112595
80.3075679159670.05717578196720.3226682152190.9932814693490.1091637456344.713139908450.0687972801792-0.0985088317807-0.1356374692340.04173569203890.02810874991970.1394868080470.623071501257-0.292787769192-0.1042710665530.328815484139-0.0628539056058-0.003217200345450.185376128505-0.002145080059180.32072972335428.5774516959-4.5264179917839.3345330767
90.712311202964-0.1019277151150.3495462680281.556348750330.1129586600152.560050106520.0872291831507-0.129980658493-0.3191265584240.03409113081750.02068984870290.1518029060581.17104582785-0.432050549529-0.1062037934820.671245265323-0.14652027661-0.009284446279560.3099120720520.008159770564340.38792133263524.0859803531-17.618714292628.0790456051
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 112 through 367 )AA112 - 3671 - 246
22chain 'A' and (resid 368 through 548 )AA368 - 548247 - 427
33chain 'B' and (resid 111 through 367 )BL111 - 3671 - 248
44chain 'B' and (resid 368 through 548 )BL368 - 548249 - 429
55chain 'C' and (resid 112 through 239 )CU112 - 2391 - 119
66chain 'C' and (resid 240 through 548 )CU240 - 548120 - 428
77chain 'D' and (resid 112 through 202 )DD112 - 2021 - 91
88chain 'D' and (resid 203 through 321 )DD203 - 32192 - 201
99chain 'D' and (resid 322 through 548 )DD322 - 548202 - 428

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