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- PDB-3kms: G62S mutant of foot-and-mouth disease virus RNA-polymerase in com... -

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Basic information

Entry
Database: PDB / ID: 3kms
TitleG62S mutant of foot-and-mouth disease virus RNA-polymerase in complex with a template- primer RNA trigonal structure
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 / 3d / polymerase / ribavirin / foot-and mouth disease virus / rna dependent rna polymerase / Transferase-RNA complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding
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 / Picornavirus coat protein / Reverse transcriptase/Diguanylate cyclase domain / 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 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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: 2.2 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 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)57,3384
Polymers57,3143
Non-polymers241
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-38 kcal/mol
Surface area20690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.951, 93.951, 99.997
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 53516.711 Da / Num. of mol.: 1 / Mutation: G62S
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.: 68 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG 4000, 0.2M magnesium acetate, 0.1M HEPES pH 7.0, 4% butyrolactone, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / 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: 2.2→30 Å / Num. obs: 26125 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.084 / Rsym value: 0.094 / Net I/σ(I): 15.8
Reflection shellResolution: 2.21→2.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3753 / Rsym value: 0.642 / % possible all: 99.4

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.4 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.922 / SU B: 15.527 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26566 1320 5.1 %RANDOM
Rwork0.23613 ---
obs0.23758 24756 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.13 Å20 Å2
2---0.25 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 251 1 68 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224101
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8582.0285614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5115475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78223.483178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41115624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1341525
X-RAY DIFFRACTIONr_chiral_restr0.0580.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023063
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.170.21768
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22796
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2221.52432
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.39123805
X-RAY DIFFRACTIONr_scbond_it0.43331978
X-RAY DIFFRACTIONr_scangle_it0.6554.51809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 84 -
Rwork0.27 1773 -
obs--98.31 %

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