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- PDB-2e9r: Foot-and-mouth disease virus RNA-dependent RNA polymerase in comp... -

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Basic information

Entry
Database: PDB / ID: 2e9r
TitleFoot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin
Components
  • 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'
  • 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3'
  • RNA-dependent RNA polymerase
KeywordsTRANSFERASE/RNA / FOOT-AND-MOUTH DISEASE VIRUS / RNA-DEPENDENT RNA POLYMERASE / 3D POLYMERASE / 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 / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing ...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 / 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 / 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
RIBAVIRIN TRIPHOSPHATE / RNA / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus C-S8c1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsFerrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Sequential structures provide insights into the fidelity of RNA replication
Authors: Ferrer-Orta, C. / Arias, A. / Perez-Luque, R. / Escarmis, C. / Domingo, E. / Verdaguer, N.
#1: 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, R. / Domingo, E. / Verdaguer, N.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 2006
Title: A comparison of viral RNA-dependent RNA polymerases
Authors: Ferrer-Orta, C. / Arias, A. / Escarmis, C. / Verdaguer, N.
#3: 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.
#4: Journal: J.Mol.Biol. / Year: 2005
Title: Mutant viral polymerase in the transition of virus to error catastrophe identifies a critical site for RNA binding
Authors: Arias, A. / Agudo, R. / Ferrer-Orta, C. / Perez-Luque, R. / Airaksinen, A. / Brocchi, E. / Domingo, E. / Verdaguer, N. / Escarmis, C.
History
DepositionJan 26, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'
B: 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3'
X: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7485
Polymers58,2403
Non-polymers5082
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.094, 94.094, 99.285
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain 5'-R(*CP*AP*UP*GP*GP*GP*CP*CP*C)-3'


Mass: 2846.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by a commercial.
#2: RNA chain 5'-R(*CP*CP*C*GP*GP*GP*CP*CP*C)-3'


Mass: 1906.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence was synthesized by a commercial.

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Protein , 1 types, 1 molecules X

#3: Protein RNA-dependent RNA polymerase


Mass: 53486.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus C-S8c1 / Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: c-s8c1 / Gene: 3D / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q0QEE1, UniProt: Q9QCE4*PLUS, RNA-directed RNA polymerase

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-RTP / RIBAVIRIN TRIPHOSPHATE


Type: RNA linking / Mass: 484.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N4O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 4K, 0.2M magnesium acetate, 0.1M sodium cacodilate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 4K11
2magnesium acetate11
3sodium cacodilate11
4HOH11
5PEG 4K12
6magnesium acetate12
7sodium cacodilate12
8HOH12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.81→30 Å / Num. all: 11820 / Num. obs: 11173 / % possible obs: 90 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.1 / Rsym value: 0.09 / Net I/σ(I): 7.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ProDCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WNE

1wne


Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.876 / SU B: 19.511 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 581 4.9 %RANDOM
Rwork0.24289 ---
obs0.24546 11173 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20.51 Å20 Å2
2--1.03 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 314 30 7 4033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0214150
X-RAY DIFFRACTIONr_bond_other_d0.0020.023537
X-RAY DIFFRACTIONr_angle_refined_deg2.1162.0475706
X-RAY DIFFRACTIONr_angle_other_deg0.98538223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9775475
X-RAY DIFFRACTIONr_chiral_restr0.1010.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024438
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02813
X-RAY DIFFRACTIONr_nbd_refined0.2790.21241
X-RAY DIFFRACTIONr_nbd_other0.2550.24644
X-RAY DIFFRACTIONr_nbtor_other0.0990.22339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.22
X-RAY DIFFRACTIONr_mcbond_it0.7941.52364
X-RAY DIFFRACTIONr_mcangle_it1.52323785
X-RAY DIFFRACTIONr_scbond_it2.1131786
X-RAY DIFFRACTIONr_scangle_it3.394.51921
LS refinement shellResolution: 2.807→2.879 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 37
Rwork0.209 780

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