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- PDB-8c2p: FMDV 3D polymerase in complex with 3B3 -

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Basic information

Entry
Database: PDB / ID: 8c2p
TitleFMDV 3D polymerase in complex with 3B3
Components
  • Protein 3B-3
  • RNA-directed RNA polymerase 3D-POL
KeywordsVIRAL PROTEIN / RNA dependent RNA polymerase FMDV Picornavirus 3B VPg
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / regulation of translation / monoatomic ion transmembrane transport ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / 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 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral ...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 / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFerrer-Orta, C. / Veraguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-117976GB-100 Spain
CitationJournal: Plos Pathog. / Year: 2023
Title: Dual role of the foot-and-mouth disease virus 3B1 protein in the replication complex: As protein primer and as an essential component to recruit 3Dpol to membranes.
Authors: Ferrer-Orta, C. / Ferrero, D.S. / Verdaguer, N.
History
DepositionDec 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase 3D-POL
B: Protein 3B-3


Theoretical massNumber of molelcules
Total (without water)56,6232
Polymers56,6232
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, the dpolymerase elute as a monomer in a superdex 75 10 300
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-4 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.512, 93.512, 100.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein RNA-directed RNA polymerase 3D-POL / P3D-POL / P56A


Mass: 54039.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: P03311, RNA-directed RNA polymerase
#2: Protein/peptide Protein 3B-3 / P3B-3 / Genome-linked protein VPg3


Mass: 2584.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus / References: UniProt: P03311
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M magnesium acetate 25% PEG 4K 0.1M HEPES pH 6.5 4% butyrolactone.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→46.76 Å / Num. obs: 43448 / % possible obs: 99.33 % / Redundancy: 6.3 % / Biso Wilson estimate: 33.98 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.05456 / Net I/σ(I): 18.93
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 4227 / CC1/2: 0.799 / CC star: 0.943 / % possible all: 98.62

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
DMphasing
SCALAdata scaling
autoPROCdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wne

1wne


Resolution: 1.85→46.76 Å / SU ML: 0.2471 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1772
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2623 2046 4.71 %
Rwork0.2426 41400 -
obs0.2436 43446 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.98 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 0 51 3756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873794
X-RAY DIFFRACTIONf_angle_d1.02955143
X-RAY DIFFRACTIONf_chiral_restr0.065561
X-RAY DIFFRACTIONf_plane_restr0.0092671
X-RAY DIFFRACTIONf_dihedral_angle_d14.44071375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.33431260.32962690X-RAY DIFFRACTION98.39
1.89-1.940.32041400.29482701X-RAY DIFFRACTION98.78
1.94-1.990.32851650.29642710X-RAY DIFFRACTION98.97
1.99-2.050.2921150.29962708X-RAY DIFFRACTION98.64
2.05-2.120.31051440.2912719X-RAY DIFFRACTION99.27
2.12-2.190.32761170.29332749X-RAY DIFFRACTION99.1
2.19-2.280.31461550.28382732X-RAY DIFFRACTION99.07
2.28-2.380.31871180.2832743X-RAY DIFFRACTION99.48
2.39-2.510.33281180.27322754X-RAY DIFFRACTION99.41
2.51-2.670.29131170.27682792X-RAY DIFFRACTION99.59
2.67-2.870.31091690.27922740X-RAY DIFFRACTION99.69
2.87-3.160.28641270.26742789X-RAY DIFFRACTION99.86
3.16-3.620.24721510.24472793X-RAY DIFFRACTION99.97
3.62-4.560.23021440.2022828X-RAY DIFFRACTION99.93
4.56-46.760.19881400.18992952X-RAY DIFFRACTION99.9

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