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- PDB-3cdw: Crystal structure of coxsackievirus B3 RNA-dependent RNA polymera... -

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Basic information

Entry
Database: PDB / ID: 3cdw
TitleCrystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with protein primer VPg and a pyrophosphate
Components
  • Protein 3B
  • RNA-directed RNA polymerase 3D-POL
KeywordsTransferase/VIRAL PROTEIN / coxsackievirus / RNA-dependent RNA polymerase / protein primer / VPg / VIZIER Viral Enzymes Involved in Replication / Transferase-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


: / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / symbiont-mediated perturbation of host gene expression / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Picornavirus coat protein VP4 superfamily / Reverse transcriptase/Diguanylate cyclase domain / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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
ACETATE ION / PYROPHOSPHATE 2- / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGruez, A. / Selisko, B. / Roberts, M. / Bricogne, G. / Bussetta, C. / Canard, B.
CitationJournal: J.Virol. / Year: 2008
Title: The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases
Authors: Gruez, A. / Selisko, B. / Roberts, M. / Bricogne, G. / Bussetta, C. / Jabafi, I. / Coutard, B. / De Palma, A.M. / Neyts, J. / Canard, B.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / 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: RNA-directed RNA polymerase 3D-POL
H: Protein 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,95643
Polymers55,6912
Non-polymers3,26541
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-86 kcal/mol
Surface area20550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.213, 74.213, 285.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AH

#1: Protein RNA-directed RNA polymerase 3D-POL


Mass: 53277.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Strain: Nancy / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(pLysS) / References: UniProt: P03313, RNA-directed RNA polymerase
#2: Protein/peptide Protein 3B / VPg


Mass: 2412.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide synthesis / References: UniProt: P03313

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Non-polymers , 5 types, 359 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 2M ammonium sulfate, 0.1M CAPS, 0.2M lithium sulfate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2006
RadiationMonochromator: Diamond (111) - Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→27.45 Å / Num. all: 28820 / Num. obs: 28791 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.45 % / Biso Wilson estimate: 56.65 Å2 / Rsym value: 0.084 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.386 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER-TNT2.3.0refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CDU

3cdu


Resolution: 2.5→27.45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2196 1451 5.06 %RANDOM
Rwork0.1753 ---
all0.1829 28765 --
obs0.1829 27251 99.78 %-
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.34454516 Å20 Å20 Å2
2---4.34454516 Å20 Å2
3---8.68909033 Å2
Refine analyzeLuzzati coordinate error obs: 0.2715 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 202 318 4339
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00841732
X-RAY DIFFRACTIONt_angle_deg1.04155512
X-RAY DIFFRACTIONt_dihedral_angle_d18.8528020
X-RAY DIFFRACTIONt_trig_c_planes0.004932
X-RAY DIFFRACTIONt_gen_planes0.015715
X-RAY DIFFRACTIONt_it1.304417320
X-RAY DIFFRACTIONt_nbd0.026885
LS refinement shellResolution: 2.5→2.65 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2553 240 5.35 %
Rwork0.2073 4246 -
all0.2162 4486 -
obs--99.78 %

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