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- PDB-6s2l: FMDV 3D polymerase crystallized in presence of (F)uridylylated VP... -

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Basic information

Entry
Database: PDB / ID: 6s2l
TitleFMDV 3D polymerase crystallized in presence of (F)uridylylated VPg peptide
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / RNA dependent RNA polymerase 3D polymerase VPg Picornavirus
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / regulation of translation / nucleoside-triphosphate phosphatase / 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 activation of host autophagy / RNA-directed RNA polymerase / 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 / 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
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVerdaguer, N. / Ferrer-Orta, C.
CitationJournal: Molecules / Year: 2019
Title: (F)uridylylated Peptides Linked to VPg1 of Foot-and- Mouth Disease Virus (FMDV): Design, Synthesis and X-Ray Crystallography of the Complexes with FMDV RNA-Dependent RNA Polymerase.
Authors: de Castro, S. / Ferrer-Orta, C. / Mills, A. / Fernandez-Cureses, G. / Gago, F. / Verdaguer, N. / Camarasa, M.J.
History
DepositionJun 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3874
Polymers54,1101
Non-polymers2763
Water2,702150
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, sdx 200 10 300
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-2 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.850, 93.850, 121.310
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 Genome polyprotein


Mass: 54110.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus (isolate -/Spain/S8c1SantaPau/1970 serotype C)
Strain: isolate -/Spain/S8c1SantaPau/1970 serotype C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03311, L-peptidase, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 30% PEG 4K, 0.1M MES pH 6.0, 4 butyrolactone

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97692 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97692 Å / Relative weight: 1
ReflectionResolution: 2.3→74.23 Å / Num. obs: 24747 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3536 / Rpim(I) all: 0.319 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U09

1u09


Resolution: 2.3→74.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 15.637 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25203 1257 5.1 %RANDOM
Rwork0.19738 ---
obs0.20011 23429 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.302 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---1.01 Å20 Å2
3---2.03 Å2
Refinement stepCycle: 1 / Resolution: 2.3→74.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 18 150 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133848
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173530
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.6435209
X-RAY DIFFRACTIONr_angle_other_deg1.1881.5768165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5421.683208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28515631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1441527
X-RAY DIFFRACTIONr_chiral_restr0.0530.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
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_it1.1643.6281903
X-RAY DIFFRACTIONr_mcbond_other1.1643.6271902
X-RAY DIFFRACTIONr_mcangle_it2.0565.4392377
X-RAY DIFFRACTIONr_mcangle_other2.0555.442378
X-RAY DIFFRACTIONr_scbond_it1.1033.7681945
X-RAY DIFFRACTIONr_scbond_other1.1033.771946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9275.5832833
X-RAY DIFFRACTIONr_long_range_B_refined4.2941.4414167
X-RAY DIFFRACTIONr_long_range_B_other4.28941.4524168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 84 -
Rwork0.262 1718 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.3134 Å / Origin y: 25.5544 Å / Origin z: 30.9492 Å
111213212223313233
T0.0782 Å2-0.0165 Å20.0059 Å2-0.0982 Å20.0093 Å2--0.0136 Å2
L1.707 °2-0.4958 °20.0879 °2-0.4043 °2-0.0988 °2--0.481 °2
S0.1009 Å °-0.041 Å °-0.0501 Å °-0.1484 Å °-0.028 Å °0.0089 Å °-0.0211 Å °0.0211 Å °-0.073 Å °

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