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- PDB-2d7s: Foot and Mouth Disease Virus RNA-dependent RNA polymerase in comp... -

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Basic information

Entry
Database: PDB / ID: 2d7s
TitleFoot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with VPg protein
Components
  • RNA-dependent RNA polymerase
  • VPg1 protein
KeywordsTRANSFERASE / Foot and mouth disease virus / RNA-dependent RNA polymerase / 3D polymerase / VPg / protein-primer
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 / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / viral protein processing / RNA helicase activity ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / viral protein processing / RNA helicase activity / host cell endoplasmic reticulum membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / 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 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 / Capsid protein VP4 superfamily, Picornavirus / Mitochondrial Import Receptor Subunit Tom20; Chain A / 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 / 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
: / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFerrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
Citation
Journal: Embo J. / Year: 2006
Title: The structure of a protein primer-polymerase complex in the initiation of genome replication
Authors: Ferrer-Orta, C. / Arias, A. / Agudo, R. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA
Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
History
DepositionNov 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
B: VPg1 protein


Theoretical massNumber of molelcules
Total (without water)55,8772
Polymers55,8772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.090, 95.090, 100.628
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 RNA-dependent RNA polymerase


Mass: 53210.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Strain: C-S8c1 / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: GenBank: 6318192, UniProt: Q9QCE4*PLUS, RNA-directed RNA polymerase
#2: Protein/peptide VPg1 protein


Mass: 2666.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase peptide synthesis
References: GenBank: 6318192, UniProt: Q9QCE4*PLUS, RNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 33% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 4% butyrolactone, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004
RadiationMonochromator: single wavelenght / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 10850 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.8
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNE

1wne


Resolution: 3→29.74 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2350327.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.294 569 5.3 %RANDOM
Rwork0.277 ---
obs0.277 10830 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.5045 Å2 / ksol: 0.307505 e/Å3
Displacement parametersBiso mean: 77 Å2
Baniso -1Baniso -2Baniso -3
1-7.67 Å210.14 Å20 Å2
2--7.67 Å20 Å2
3----15.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 0 3855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it3.082
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.452 71 4.1 %
Rwork0.377 1650 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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