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- PDB-3kna: M296I mutant of foot-and-mouth disease virus RNA-polymerase in co... -

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Basic information

Entry
Database: PDB / ID: 3kna
TitleM296I mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA
Components
  • 3D polymerase
  • RNA (5'-R(*AP*UP*GP*GP*GP*CP*C)-3')
  • RNA (5'-R(*GP*GP*CP*CP*C)-3')
KeywordsTransferase/RNA / RNA dependent RNA polymerase / 3d polymerase / foot-and-mouth disease virus / ribavirin / Transferase-RNA complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane ...symbiont-mediated perturbation of host chromatin organization / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Mitochondrial Import Receptor Subunit Tom20; Chain A / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Reverse transcriptase/Diguanylate cyclase domain / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFerrer-Orta, C. / Verdaguer, N. / Perez-Luque, R.
CitationJournal: J.Virol. / Year: 2010
Title: Structure of foot-and-mouth disease virus mutant polymerases with reduced sensitivity to ribavirin
Authors: Ferrer-Orta, C. / Sierra, M. / Agudo, R. / de la Higuera, I. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
History
DepositionNov 12, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3D polymerase
B: RNA (5'-R(*AP*UP*GP*GP*GP*CP*C)-3')
C: RNA (5'-R(*GP*GP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2904
Polymers57,2663
Non-polymers241
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-39 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.565, 93.565, 120.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 3D polymerase / rna dependent rna polymerase


Mass: 53468.645 Da / Num. of mol.: 1 / Mutation: M296I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type C / Strain: C-S8c1 / Gene: 3D / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9QCE3, RNA-directed RNA polymerase
#2: RNA chain RNA (5'-R(*AP*UP*GP*GP*GP*CP*C)-3')


Mass: 2236.395 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*GP*GP*CP*CP*C)-3')


Mass: 1561.000 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 46.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 4000, 0.1M HEPES pH 7.0, 4% butyrolactone, 0.2M Magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→74 Å / Num. obs: 13868 / % possible obs: 99.5 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNE

1wne


Resolution: 2.8→74 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.875 / SU B: 37.117 / SU ML: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27978 690 5 %RANDOM
Rwork0.23859 ---
obs0.24062 13086 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.621 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 251 1 38 4046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0224126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.432.0285644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0765475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.16823.443183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30215637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6261527
X-RAY DIFFRACTIONr_chiral_restr0.0310.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0213085
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1391.52366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.24923809
X-RAY DIFFRACTIONr_scbond_it0.07831760
X-RAY DIFFRACTIONr_scangle_it0.1444.51835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 54 -
Rwork0.331 945 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 21.7407 Å / Origin y: 25.6187 Å / Origin z: 30.962 Å
111213212223313233
T0.2667 Å2-0.0481 Å20.0273 Å2-0.1854 Å20.0536 Å2--0.1587 Å2
L2.7968 °2-1.2791 °2-0.3159 °2-1.2248 °20.1131 °2--0.8115 °2
S0.1875 Å °0.077 Å °0.0485 Å °-0.4551 Å °-0.0902 Å °-0.0795 Å °-0.0702 Å °0.0606 Å °-0.0973 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 476
2X-RAY DIFFRACTION1B903 - 909
3X-RAY DIFFRACTION1C916 - 920

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