[English] 日本語
Yorodumi
- PDB-9cll: Plasmodium falciparum tyrosyl-tRNA synthetase in complex with ML4... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cll
TitlePlasmodium falciparum tyrosyl-tRNA synthetase in complex with ML471-Tyr
Componentstyrosine--tRNA ligase
KeywordsLIGASE/INHIBITOR / Inhibitor complex / LIGASE / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


tyrosyl-tRNA aminoacylation / tyrosine-tRNA ligase / tyrosine-tRNA ligase activity / host cell cytosol / host cell surface receptor binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Tyrosine-tRNA ligase, archaeal/eukaryotic-type / : / Aminoacyl-tRNA synthetase, class Ic / tRNA synthetases class I (W and Y) / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
: / MALONATE ION / tyrosine--tRNA ligase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTai, C.W. / Dogovski, C. / Xie, S.C. / Tilley, L. / Griffin, M.D.W.
Funding support Japan, Australia, 2items
OrganizationGrant numberCountry
Global Health Innovative Technology FundH2019-104 Japan
National Health and Medical Research Council (NHMRC, Australia)APP2022075 Australia
CitationJournal: Plos Pathog. / Year: 2024
Title: A potent and selective reaction hijacking inhibitor of Plasmodium falciparum tyrosine tRNA synthetase exhibits single dose oral efficacy in vivo.
Authors: Xie, S.C. / Tai, C.W. / Morton, C.J. / Ma, L. / Huang, S.C. / Wittlin, S. / Du, Y. / Hu, Y. / Dogovski, C. / Salimimarand, M. / Griffin, R. / England, D. / de la Cruz, E. / Deni, I. / Yeo, T. ...Authors: Xie, S.C. / Tai, C.W. / Morton, C.J. / Ma, L. / Huang, S.C. / Wittlin, S. / Du, Y. / Hu, Y. / Dogovski, C. / Salimimarand, M. / Griffin, R. / England, D. / de la Cruz, E. / Deni, I. / Yeo, T. / Burkhard, A.Y. / Striepen, J. / Schindler, K.A. / Crespo, B. / Gamo, F.J. / Khandokar, Y. / Hutton, C.A. / Rabie, T. / Birkholtz, L.M. / Famodimu, M.T. / Delves, M.J. / Bolsher, J. / Koolen, K.M.J. / van der Laak, R. / Aguiar, A.C.C. / Pereira, D.B. / Guido, R.V.C. / Creek, D.J. / Fidock, D.A. / Dick, L.R. / Brand, S.L. / Gould, A.E. / Langston, S. / Griffin, M.D.W. / Tilley, L.
History
DepositionJul 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tyrosine--tRNA ligase
B: tyrosine--tRNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,49912
Polymers87,0282
Non-polymers1,47010
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-80 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.208, 47.271, 140.512
Angle α, β, γ (deg.)90.000, 94.628, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-697-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 17 through 243 or resid 253 through 372 or resid 401 through 402))
d_2ens_1(chain "B" and (resid 17 through 372 or resid 401 through 402))

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_11LYSLYSGLUGLUAA17 - 24317 - 243
d_12GLUGLUTHRTHRAA253 - 372253 - 372
d_13A1AZGA1AZGA1AZGA1AZGAC401
d_14MLIMLIMLIMLIAD402
d_21LYSLYSTHRTHRBB17 - 37217 - 372
d_22A1AZGA1AZGA1AZGA1AZGBG401
d_23MLIMLIMLIMLIBH402

NCS oper: (Code: givenMatrix: (-0.76385350733556, 0.64153708581083, -0.070412973666122), (0.62454814359559, 0.70727193330967, -0.33121900411012), (-0.16268815464705, -0.29697908997393, -0. ...NCS oper: (Code: given
Matrix: (-0.76385350733556, 0.64153708581083, -0.070412973666122), (0.62454814359559, 0.70727193330967, -0.33121900411012), (-0.16268815464705, -0.29697908997393, -0.94092294288948)
Vector: -1.0094459572536, 14.705270512129, 72.902806742877)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein tyrosine--tRNA ligase / Tyrosyl-tRNA synthetase


Mass: 43514.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_0807900 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IAR7, tyrosine-tRNA ligase

-
Non-polymers , 5 types, 390 molecules

#2: Chemical ChemComp-A1AZG / {(2R,3S,4R,5R)-5-[4-amino-3-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]-3,4-dihydroxyoxolan-2-yl}methyl [(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]sulfamate


Mass: 551.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29N7O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5M sodium malonate, pH 6

-
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: Jun 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→46.68 Å / Num. obs: 84432 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.82 Å / Num. unique obs: 4481 / CC1/2: 0.838

-
Processing

Software
NameVersionClassification
PHENIX1.21.1.5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.68 Å / SU ML: 0.2321 / Cross valid method: FREE R-VALUE / σ(F): 1.71 / Phase error: 24.3284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2198 4177 4.95 %
Rwork0.183 80213 -
obs0.1848 84390 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5683 0 96 380 6159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01725887
X-RAY DIFFRACTIONf_angle_d1.50317926
X-RAY DIFFRACTIONf_chiral_restr0.0908854
X-RAY DIFFRACTIONf_plane_restr0.01151003
X-RAY DIFFRACTIONf_dihedral_angle_d19.39652265
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.5136648580525 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35171360.31722698X-RAY DIFFRACTION99.93
1.82-1.840.36141330.29932579X-RAY DIFFRACTION99.85
1.84-1.860.34841230.2892688X-RAY DIFFRACTION99.82
1.86-1.890.29991630.26882626X-RAY DIFFRACTION99.96
1.89-1.910.3261300.24932641X-RAY DIFFRACTION99.89
1.91-1.940.2861420.23622652X-RAY DIFFRACTION99.96
1.94-1.970.2931530.2272699X-RAY DIFFRACTION100
1.97-20.26761420.222608X-RAY DIFFRACTION99.96
2-2.030.26691470.22882654X-RAY DIFFRACTION99.79
2.03-2.060.26451400.20752665X-RAY DIFFRACTION99.96
2.06-2.10.25031350.19162660X-RAY DIFFRACTION100
2.1-2.130.25991260.19262665X-RAY DIFFRACTION100
2.13-2.180.2541580.18722640X-RAY DIFFRACTION99.96
2.18-2.220.21551530.18772640X-RAY DIFFRACTION99.96
2.22-2.270.24131290.18792704X-RAY DIFFRACTION99.96
2.27-2.320.25931370.18842641X-RAY DIFFRACTION100
2.32-2.380.2521350.18492667X-RAY DIFFRACTION99.96
2.38-2.440.22251400.18682662X-RAY DIFFRACTION99.82
2.44-2.510.26351130.18862716X-RAY DIFFRACTION99.79
2.51-2.60.25431290.19822694X-RAY DIFFRACTION99.96
2.6-2.690.25491380.22312658X-RAY DIFFRACTION99.96
2.69-2.80.24081350.20962688X-RAY DIFFRACTION99.89
2.8-2.920.20491600.19592652X-RAY DIFFRACTION99.86
2.92-3.080.21371400.1982657X-RAY DIFFRACTION99.89
3.08-3.270.23781440.20052694X-RAY DIFFRACTION99.89
3.27-3.520.21611290.18042713X-RAY DIFFRACTION99.93
3.52-3.880.2211260.16392693X-RAY DIFFRACTION99.72
3.88-4.440.17321400.14332717X-RAY DIFFRACTION99.86
4.44-5.590.17241520.15142717X-RAY DIFFRACTION99.14
5.59-46.680.18251490.16352825X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: -2.5313305347518 Å / Origin y: -0.8840572344561 Å / Origin z: 39.271766436477 Å
111213212223313233
T0.20772189955705 Å20.005414554471691 Å20.0076010382049863 Å2-0.36084058352957 Å2-0.0069099430198071 Å2--0.29211894737101 Å2
L0.75902173027855 °2-0.31530254652524 °20.79712875071617 °2-0.52541962344154 °2-0.38598198693262 °2--1.219280399272 °2
S0.076003311258432 Å °0.018130758952401 Å °-0.15072082286854 Å °-0.10229631506403 Å °0.07467473687633 Å °0.12972279024716 Å °0.059493643873776 Å °-0.14492188848826 Å °-0.13140297990417 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more