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- PDB-4a5u: Turnip yellow mosaic virus proteinase and Escherichia coli 30S ri... -

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Basic information

Entry
Database: PDB / ID: 4a5u
TitleTurnip yellow mosaic virus proteinase and Escherichia coli 30S ribosomal S15
Components
  • 30S RIBOSOMAL PROTEIN S15
  • RNA REPLICASE POLYPROTEIN
KeywordsTRANSFERASE/RNA BINDING PROTEIN / TRANSFERASE-RNA BINDING PROTEIN COMPLEX / CYSTEINE PROTEINASE
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. / S15/NS1, RNA-binding / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain ...Tymovirus endopeptidases / Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / S15/NS1, RNA-binding / 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 / Helix Hairpins / (+) 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA replicase polyprotein
Similarity search - Component
Biological speciesTURNIP YELLOW MOSAIC VIRUS
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsRobin, C. / Beaurepaire, L. / Bressanelli, S.
Citation
Journal: Plos Pathog. / Year: 2013
Title: A Compact Viral Processing Proteinase/Ubiquitin Hydrolase from the Otu Family.
Authors: Lombardi, C. / Ayach, M. / Beaurepaire, L. / Chenon, M. / Andreani, J. / Guerois, R. / Jupin, I. / Bressanelli, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: In Praise of Impurity: 30S Ribosomal S15 Protein-Assisted Crystallization of Turnip Yellow Mosaic Virus Proteinase.
Authors: Robin, C. / Beaurepaire, L. / Chenon, M. / Jupin, I. / Bressanelli, S.
History
DepositionOct 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA REPLICASE POLYPROTEIN
B: 30S RIBOSOMAL PROTEIN S15


Theoretical massNumber of molelcules
Total (without water)27,9382
Polymers27,9382
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.200, 135.200, 41.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2026-

HOH

21B-2037-

HOH

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Components

#1: Protein RNA REPLICASE POLYPROTEIN


Mass: 17778.873 Da / Num. of mol.: 1
Fragment: POLYPROTEIN PROCESSING PROTEINASE DOMAIN, RESIDUES 728-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TURNIP YELLOW MOSAIC VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10358, RNA-directed RNA polymerase
#2: Protein 30S RIBOSOMAL PROTEIN S15


Mass: 10159.621 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-89 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / References: UniProt: E8Y371
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.99 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5 2.5 M AMMONIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2→39.5 Å / Num. obs: 29613 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 27.24 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
autoSHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2→39.029 Å / SU ML: 0.56 / σ(F): 2 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 2275 7.7 %
Rwork0.1678 --
obs0.1704 29610 99.04 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.886 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.7292 Å20 Å20 Å2
2--2.7292 Å20 Å2
3----1.6959 Å2
Refinement stepCycle: LAST / Resolution: 2→39.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 0 194 1991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071879
X-RAY DIFFRACTIONf_angle_d1.052558
X-RAY DIFFRACTIONf_dihedral_angle_d13.509722
X-RAY DIFFRACTIONf_chiral_restr0.069297
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.27692200.22242719X-RAY DIFFRACTION99
2.0715-2.15440.24022230.20012691X-RAY DIFFRACTION99
2.1544-2.25250.24692200.1892720X-RAY DIFFRACTION99
2.2525-2.37120.19792410.16852720X-RAY DIFFRACTION99
2.3712-2.51970.22222220.16362710X-RAY DIFFRACTION99
2.5197-2.71420.20762280.16762747X-RAY DIFFRACTION100
2.7142-2.98730.2062340.17542748X-RAY DIFFRACTION99
2.9873-3.41940.21222230.17042732X-RAY DIFFRACTION99
3.4194-4.30720.1772280.1482746X-RAY DIFFRACTION98
4.3072-39.03630.17732360.16092802X-RAY DIFFRACTION98
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)
12.0407-1.5638-0.04922.23850.38221.0976-0.0326-0.00520.1392-0.01470.0294-0.0995-0.02280.09830.00610.08020.0277-0.00560.13630.00730.105511.18267.319221.2342
22.1414-1.1174-0.28841.63610.22171.55510.14260.3283-0.3821-0.2467-0.15350.23030.1386-0.03610.00240.20010.1137-0.03590.2949-0.06570.163824.890343.258911.7642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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