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- PDB-8s0v: Crystal structure of Cryptosporidium parvum - Trypanosoma cruzi m... -

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Basic information

Entry
Database: PDB / ID: 8s0v
TitleCrystal structure of Cryptosporidium parvum - Trypanosoma cruzi mutant lysyl tRNA synthetase in complex with inhibitor
ComponentsLysine--tRNA ligase
KeywordsLIGASE / TRNA binding
Function / homology
Function and homology information


lysine-tRNA ligase / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / tRNA binding / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / 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. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysyl-tRNA synthetase, class II, C-terminal / 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
: / LYSINE / Lysine--tRNA ligase
Similarity search - Component
Biological speciesCryptosporidium parvum Iowa (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDawson, A. / Wyllie, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust218448/Z/19/Z United Kingdom
CitationJournal: Sci Transl Med / Year: 2025
Title: Antitrypanosomal quinazolines targeting lysyl-tRNA synthetase show partial efficacy in a mouse model of acute Chagas disease.
Authors: Tulloch, L.B. / Tawell, H. / Taylor, A.E. / Lima, M.L. / Dawson, A. / Carvalho, S. / Wall, R.J. / Corpas-Lopez, V. / Dey, G. / Duggan, J. / Magalhaes, L.G. / Torrie, L.S. / Frame, L. / ...Authors: Tulloch, L.B. / Tawell, H. / Taylor, A.E. / Lima, M.L. / Dawson, A. / Carvalho, S. / Wall, R.J. / Corpas-Lopez, V. / Dey, G. / Duggan, J. / Magalhaes, L.G. / Torrie, L.S. / Frame, L. / Robinson, D. / Patterson, S. / Tinti, M. / Weaver, G.W. / Robinson, W.J. / Cal, M. / Kaiser, M. / Maser, P. / Sjo, P. / Perry, B. / Kelly, J.M. / Francisco, A.F. / Bhambra, A.S. / Wyllie, S.
History
DepositionFeb 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 2.0Jul 9, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_asym / struct_mon_prot_cis / struct_ncs_dom / struct_ncs_dom_lim
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.overall_SU_B / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_restr_ncs.rms_dev_position / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_asym.entity_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ncs_dom.details / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Description: Ligand geometry
Details: OXT atom of bound lysine was lost during deposition and has been replaced.
Provider: author / Type: Coordinate replacement
Revision 2.1Jul 16, 2025Group: 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: Lysine--tRNA ligase
B: Lysine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,02013
Polymers123,3952
Non-polymers1,62611
Water13,583754
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.136, 116.697, 142.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-606-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 45 - 544 / Label seq-ID: 22 - 521

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase


Mass: 61697.266 Da / Num. of mol.: 2 / Mutation: I538L, A309S, M310V, I290L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum Iowa (eukaryote)
Gene: cgd4_2370 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CR27, lysine-tRNA ligase

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Non-polymers , 6 types, 765 molecules

#2: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-A1H4X / ~{N}7-cyclopentyl-5,6,8-tris(fluoranyl)-2-methyl-quinazoline-4,7-diamine


Mass: 296.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15F3N4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8
PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.6→58.35 Å / Num. obs: 160925 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Χ2: 1 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 62276 / CC1/2: 0.628 / Rpim(I) all: 0.635 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→58.35 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.721 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.083 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2083 8146 5.065 %
Rwork0.184 152691 -
all0.185 --
obs-160837 99.697 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å2-0 Å20 Å2
2--0.809 Å2-0 Å2
3----0.872 Å2
Refinement stepCycle: LAST / Resolution: 1.6→58.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8031 0 109 754 8894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0128347
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167884
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.85711256
X-RAY DIFFRACTIONr_angle_other_deg0.6471.76518249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8945991
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.7525.18554
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.469102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55101508
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.22610395
X-RAY DIFFRACTIONr_chiral_restr0.1070.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021877
X-RAY DIFFRACTIONr_nbd_refined0.2160.21494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.27333
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24026
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2547
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.215
X-RAY DIFFRACTIONr_nbd_other0.1530.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.227
X-RAY DIFFRACTIONr_mcbond_it2.1322.2293973
X-RAY DIFFRACTIONr_mcbond_other2.1322.2283971
X-RAY DIFFRACTIONr_mcangle_it2.9093.9964953
X-RAY DIFFRACTIONr_mcangle_other2.9093.9964954
X-RAY DIFFRACTIONr_scbond_it3.4662.5744374
X-RAY DIFFRACTIONr_scbond_other3.4642.5754371
X-RAY DIFFRACTIONr_scangle_it5.1374.5636301
X-RAY DIFFRACTIONr_scangle_other5.1364.5636296
X-RAY DIFFRACTIONr_lrange_it6.13822.8579410
X-RAY DIFFRACTIONr_lrange_other6.11322.5059252
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0516062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088310.05008
12AX-RAY DIFFRACTIONLocal ncs0.088310.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.2945730.2810785X-RAY DIFFRACTION96.1239
1.642-1.6860.2785670.25310924X-RAY DIFFRACTION99.8696
1.686-1.7350.2415490.22210630X-RAY DIFFRACTION100
1.735-1.7890.2525290.21610405X-RAY DIFFRACTION99.9817
1.789-1.8470.2345330.1979972X-RAY DIFFRACTION99.981
1.847-1.9120.2235220.1919737X-RAY DIFFRACTION100
1.912-1.9840.2065380.1819324X-RAY DIFFRACTION99.9899
1.984-2.0650.2124730.1829009X-RAY DIFFRACTION100
2.065-2.1570.2334640.1828704X-RAY DIFFRACTION100
2.157-2.2620.1974280.1788289X-RAY DIFFRACTION99.9771
2.262-2.3840.1864260.1687907X-RAY DIFFRACTION100
2.384-2.5280.2074050.1697489X-RAY DIFFRACTION100
2.528-2.7030.2163970.1797036X-RAY DIFFRACTION100
2.703-2.9190.2293600.186595X-RAY DIFFRACTION100
2.919-3.1960.2033210.1866051X-RAY DIFFRACTION100
3.196-3.5720.2062960.1885510X-RAY DIFFRACTION100
3.572-4.1220.1842570.1734917X-RAY DIFFRACTION99.9807
4.122-5.0430.1812360.1544158X-RAY DIFFRACTION100
5.043-7.1050.2161540.1963320X-RAY DIFFRACTION100
7.105-58.350.1691180.1811930X-RAY DIFFRACTION99.9024

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