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- PDB-9csh: Turnip Yellow Mosaic Virus (TYMV) protease (PRO) bound to a ubiqu... -

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Basic information

Entry
Database: PDB / ID: 9csh
TitleTurnip Yellow Mosaic Virus (TYMV) protease (PRO) bound to a ubiquitin variant (UbV3)
Components
  • Methyltransferase/Protease/Ubiquitinyl hydrolase
  • Ubiquitin Variant UbV3
KeywordsVIRAL PROTEIN / Turnip Yellow Mosaic Virus / TYMV / viral protease / PRO / deubiquitinase / ubiquitin variant / UbV
Function / homology
Function and homology information


mRNA methyltransferase activity / mRNA modification / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA-directed RNA polymerase ...mRNA methyltransferase activity / mRNA modification / RNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase ...Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral superfamily 1 RNA helicase core domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Non-structural replication polyprotein
Similarity search - Component
Biological speciesTurnip yellow mosaic virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, K. / Mark, B.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-05682 Canada
Citation
Journal: Plos Pathog. / Year: 2025
Title: Suppressing Tymovirus replication in plants using a variant of ubiquitin.
Authors: De Silva, A. / Kim, K. / Weiland, J. / Hwang, J. / Chung, J. / Pereira, H.S. / Patel, T.R. / Teyra, J. / Patel, A. / Mira, M.M. / Khajehpour, M. / Bolton, M. / Stasolla, C. / Sidhu, S.S. / Mark, B.L.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase/Protease/Ubiquitinyl hydrolase
B: Ubiquitin Variant UbV3
C: Methyltransferase/Protease/Ubiquitinyl hydrolase
D: Ubiquitin Variant UbV3


Theoretical massNumber of molelcules
Total (without water)59,0004
Polymers59,0004
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9720 Å2
ΔGint-49 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.006, 89.664, 137.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Methyltransferase/Protease/Ubiquitinyl hydrolase / 98 kDa protein / MET/PRO


Mass: 17647.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Turnip yellow mosaic virus / Production host: Escherichia coli (E. coli)
References: UniProt: P10358, Transferases; Transferring one-carbon groups; Methyltransferases, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ubiquitin Variant UbV3


Mass: 11852.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has ligand of interestY
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5M ammonium sulphate, 100mM Bis-Tris pH 6.5, 100mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→45.83 Å / Num. obs: 11252 / % possible obs: 99.4 % / Redundancy: 13.8 % / Biso Wilson estimate: 36.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.042 / Rrim(I) all: 0.157 / Net I/σ(I): 16.6
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1065 / CC1/2: 0.896 / Rpim(I) all: 0.166 / Rrim(I) all: 0.62

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35.5 Å / SU ML: 0.3819 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2778 1122 9.99 %
Rwork0.2291 10104 -
obs0.2339 11226 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 8 0 3456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313533
X-RAY DIFFRACTIONf_angle_d0.57994816
X-RAY DIFFRACTIONf_chiral_restr0.0432564
X-RAY DIFFRACTIONf_plane_restr0.0043630
X-RAY DIFFRACTIONf_dihedral_angle_d15.20391338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.930.3691350.3181211X-RAY DIFFRACTION96.7
2.93-3.080.36581370.29831243X-RAY DIFFRACTION99.78
3.08-3.280.34781390.27271241X-RAY DIFFRACTION99.78
3.28-3.530.31251380.26741250X-RAY DIFFRACTION99.93
3.53-3.880.29281410.23881266X-RAY DIFFRACTION99.93
3.88-4.440.24051420.19231274X-RAY DIFFRACTION99.93
4.44-5.590.21471420.1771279X-RAY DIFFRACTION100
5.6-35.50.22541480.1941340X-RAY DIFFRACTION99.73

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