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- PDB-4y2a: Crystal Structure of Coxsackie Virus B3 3D polymerase in complex ... -

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Basic information

Entry
Database: PDB / ID: 4y2a
TitleCrystal Structure of Coxsackie Virus B3 3D polymerase in complex with GPC-N114 inhibitor
Components3D polymerase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Polymerase / Picornavirus / Coxsackievirus / GPC-N114 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host transcription / 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 ...symbiont-mediated perturbation of host transcription / 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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host NF-kappaB cascade / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein ...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 / Picornavirus coat protein / 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) / 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. / 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
Chem-1FS / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVives-Adrian, L. / Ferrer-Orta, C. / Verdaguer, N.
CitationJournal: Plos Pathog. / Year: 2015
Title: The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family.
Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, ...Authors: van der Linden, L. / Vives-Adrian, L. / Selisko, B. / Ferrer-Orta, C. / Liu, X. / Lanke, K. / Ulferts, R. / De Palma, A.M. / Tanchis, F. / Goris, N. / Lefebvre, D. / De Clercq, K. / Leyssen, P. / Lacroix, C. / Purstinger, G. / Coutard, B. / Canard, B. / Boehr, D.D. / Arnold, J.J. / Cameron, C.E. / Verdaguer, N. / Neyts, J. / van Kuppeveld, F.J.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: 3D polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,28711
Polymers53,0021
Non-polymers1,28510
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-63 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.740, 74.740, 289.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 3D polymerase


Mass: 53001.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 / Production host: Escherichia coli (E. coli) / References: UniProt: P03313
#2: Chemical ChemComp-1FS / 2,2'-[(4-chlorobenzene-1,2-diyl)bis(oxy)]bis(5-nitrobenzonitrile)


Mass: 436.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C20H9ClN4O6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris pH 7.5, 24.5% (w/v) glycerol, 1.29 M ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.977 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.9→72.4 Å / Num. obs: 18099 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.081 / Rsym value: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.415 / Rsym value: 0.357 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DDK

3ddk


Resolution: 2.9→72.36 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.271 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.695 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25049 979 5.1 %RANDOM
Rwork0.19761 ---
obs0.20025 18099 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.837 Å2
Baniso -1Baniso -2Baniso -3
1-3.51 Å20 Å20 Å2
2--3.51 Å2-0 Å2
3----7.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 80 25 3832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193912
X-RAY DIFFRACTIONr_bond_other_d0.0010.023663
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9775294
X-RAY DIFFRACTIONr_angle_other_deg1.07238457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6485467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02723.736174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41815669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8381520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
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_it3.7835.2711865
X-RAY DIFFRACTIONr_mcbond_other3.7695.2691864
X-RAY DIFFRACTIONr_mcangle_it5.8027.9022330
X-RAY DIFFRACTIONr_mcangle_other5.8027.9052331
X-RAY DIFFRACTIONr_scbond_it4.6595.9062047
X-RAY DIFFRACTIONr_scbond_other4.6525.9062047
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.48.6372964
X-RAY DIFFRACTIONr_long_range_B_refined9.81943.3714434
X-RAY DIFFRACTIONr_long_range_B_other9.81943.3724433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 71 -
Rwork0.285 1299 -
obs--100 %

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