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- PDB-5lwa: TURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, I847A ... -

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Basic information

Entry
Database: PDB / ID: 5lwa
TitleTURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, I847A MUTANT
ComponentsRNA replicase polyprotein
KeywordsHYDROLASE / CYSTEINE PROTEASE / DEUBIQUITINASE / VIRUS REPLICASE POLYPROTEIN
Function / homology
Function and homology information


mRNA methyltransferase activity / 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 / viral RNA genome replication ...mRNA methyltransferase activity / 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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
Tymovirus endopeptidases / 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 endopeptidases / 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 / Cathepsin B; Chain A / (+) 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
RNA replicase polyprotein
Similarity search - Component
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsAyach, M. / Bressanelli, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-011 France
Citation
Journal: PLoS Pathog. / Year: 2017
Title: A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase.
Authors: Jupin, I. / Ayach, M. / Jomat, L. / Fieulaine, S. / Bressanelli, S.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization of mutants of Turnip yellow mosaic virus protease/ubiquitin hydrolase designed to prevent protease self-recognition.
Authors: Ayach, M. / Bressanelli, S.
History
DepositionSep 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
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
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA replicase polyprotein
B: RNA replicase polyprotein


Theoretical massNumber of molelcules
Total (without water)35,2112
Polymers35,2112
Non-polymers00
Water3,405189
1
A: RNA replicase polyprotein


Theoretical massNumber of molelcules
Total (without water)17,6061
Polymers17,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA replicase polyprotein


Theoretical massNumber of molelcules
Total (without water)17,6061
Polymers17,6061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.722, 39.677, 72.699
Angle α, β, γ (deg.)90.00, 121.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA replicase polyprotein / 206 kDa polyprotein


Mass: 17605.596 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, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on acid ...References: UniProt: P10358, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M trisodium citrate pH 5.6, 0.2 M ammonium acetate, 18%(w/v) PEG 4000, 5%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.653→50 Å / Num. obs: 38202 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06302 / Net I/σ(I): 11.8
Reflection shellResolution: 1.653→1.712 Å / Rmerge(I) obs: 0.9332 / Num. unique all: 3525

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LW5

5lw5


Resolution: 1.653→37.421 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.58
RfactorNum. reflection% reflection
Rfree0.2013 2928 7.67 %
Rwork0.1691 --
obs0.1716 38165 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.653→37.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2289 0 0 189 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062384
X-RAY DIFFRACTIONf_angle_d0.8363281
X-RAY DIFFRACTIONf_dihedral_angle_d9.6211462
X-RAY DIFFRACTIONf_chiral_restr0.049387
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6532-1.68030.37931050.38451424X-RAY DIFFRACTION86
1.6803-1.70930.33451430.35051664X-RAY DIFFRACTION98
1.7093-1.74040.34291440.311649X-RAY DIFFRACTION98
1.7404-1.77390.33921260.27451665X-RAY DIFFRACTION99
1.7739-1.81010.25821530.22941683X-RAY DIFFRACTION98
1.8101-1.84940.2841440.20891635X-RAY DIFFRACTION99
1.8494-1.89250.20911230.19661699X-RAY DIFFRACTION99
1.8925-1.93980.21581470.18311658X-RAY DIFFRACTION99
1.9398-1.99220.22331400.17931681X-RAY DIFFRACTION99
1.9922-2.05080.20561380.17231692X-RAY DIFFRACTION99
2.0508-2.1170.22291380.16921686X-RAY DIFFRACTION99
2.117-2.19270.20861470.17171665X-RAY DIFFRACTION99
2.1927-2.28050.20111340.1661696X-RAY DIFFRACTION99
2.2805-2.38420.20151460.16191700X-RAY DIFFRACTION100
2.3842-2.50990.20931420.16611714X-RAY DIFFRACTION100
2.5099-2.66710.18181400.17031687X-RAY DIFFRACTION99
2.6671-2.8730.21591400.17831703X-RAY DIFFRACTION100
2.873-3.1620.19761430.16641706X-RAY DIFFRACTION99
3.162-3.61920.18661470.15311722X-RAY DIFFRACTION99
3.6192-4.55850.14371390.13291714X-RAY DIFFRACTION99
4.5585-37.43080.1981490.15181794X-RAY DIFFRACTION100
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)
12.6946-1.1104-0.5051.47150.71661.63180.11170.32330.0616-0.1068-0.0767-0.103-0.09230.0929-0.02960.16680.0047-0.00810.13490.02270.175760.3717-22.6506-41.0291
26.07082.38540.39861.9313-0.21232.16140.1425-0.5947-0.01840.0148-0.2137-0.1249-0.11950.20210.040.1878-0.0398-0.00910.2968-0.00450.206377.3502-35.9958-14.0733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

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