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- PDB-5lw5: TURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, DELTAC... -

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Basic information

Entry
Database: PDB / ID: 5lw5
TitleTURNIP YELLOW MOSAIC VIRUS PROTEASE/DEUBIQUITINASE DOMAIN, DELTAC5 MUTANT
ComponentsRNA replicase polyprotein
KeywordsHYDROLASE / CYSTEINE PROTEASE / DEUBIQUITINASE / VIRUS REPLICASE POLYPROTEIN
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
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 core domain / 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
Non-structural replication polyprotein
Similarity search - Component
Biological speciesTurnip yellow mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 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)34,2402
Polymers34,2402
Non-polymers00
Water2,702150
1
A: RNA replicase polyprotein


Theoretical massNumber of molelcules
Total (without water)17,1201
Polymers17,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA replicase polyprotein


Theoretical massNumber of molelcules
Total (without water)17,1201
Polymers17,1201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.460, 39.695, 72.864
Angle α, β, γ (deg.)90.00, 122.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA replicase polyprotein / 206 kDa polyprotein


Mass: 17120.035 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.: 150 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M trisodium citrate pH 5.6, 0.2 M ammonium acetate, 15%(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: 1.649→50 Å / Num. obs: 39006 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06178 / Net I/σ(I): 11.2
Reflection shellResolution: 1.649→1.708 Å / Rmerge(I) obs: 0.6237 / Num. unique all: 3797

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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: 4a5u

4a5u


Resolution: 1.649→37.452 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.78
RfactorNum. reflection% reflection
Rfree0.2346 2971 7.65 %
Rwork0.2003 --
obs0.2029 38838 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.649→37.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 0 150 2401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052356
X-RAY DIFFRACTIONf_angle_d0.813246
X-RAY DIFFRACTIONf_dihedral_angle_d9.3891437
X-RAY DIFFRACTIONf_chiral_restr0.048383
X-RAY DIFFRACTIONf_plane_restr0.005429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.67640.40961340.42571613X-RAY DIFFRACTION95
1.6764-1.70530.45921350.38711712X-RAY DIFFRACTION99
1.7053-1.73630.37321500.35721703X-RAY DIFFRACTION99
1.7363-1.76970.37091300.33321692X-RAY DIFFRACTION99
1.7697-1.80580.36841470.29411718X-RAY DIFFRACTION99
1.8058-1.84510.32231400.25321669X-RAY DIFFRACTION99
1.8451-1.8880.27581380.24961739X-RAY DIFFRACTION99
1.888-1.93520.27381440.22491672X-RAY DIFFRACTION99
1.9352-1.98750.28991370.22271721X-RAY DIFFRACTION99
1.9875-2.0460.23771330.21781673X-RAY DIFFRACTION99
2.046-2.11210.27371440.23091714X-RAY DIFFRACTION99
2.1121-2.18750.32411460.241704X-RAY DIFFRACTION98
2.1875-2.27510.26941430.24321650X-RAY DIFFRACTION98
2.2751-2.37860.24311380.23311708X-RAY DIFFRACTION98
2.3786-2.5040.25331440.21551693X-RAY DIFFRACTION98
2.504-2.66090.22611430.20781700X-RAY DIFFRACTION99
2.6609-2.86620.25291400.19811723X-RAY DIFFRACTION100
2.8662-3.15450.22871460.18551735X-RAY DIFFRACTION100
3.1545-3.61070.19471480.16391758X-RAY DIFFRACTION100
3.6107-4.54780.15981410.14941751X-RAY DIFFRACTION100
4.5478-37.46190.20121500.16431819X-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)
12.2957-0.8303-0.25371.27590.3011.37570.08250.28350.0548-0.1364-0.0527-0.1712-0.04590.0982-0.03490.1810.00370.03180.1890.0210.236360.2616-22.6792-40.7896
24.71881.44120.1591.0529-0.40461.7670.1632-0.57330.245-0.0098-0.2336-0.0155-0.14860.28870.0470.2586-0.04340.04390.4224-0.03990.325577.4487-35.8727-13.6106
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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