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- PDB-9fwc: Coxsackievirus B3 3C protease in C121 spacegroup -

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Basic information

Entry
Database: PDB / ID: 9fwc
TitleCoxsackievirus B3 3C protease in C121 spacegroup
ComponentsGenome polyprotein
KeywordsHYDROLASE / Coxsackievirus B clade 3C protease
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / symbiont-mediated suppression of host gene expression / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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) ...Picornavirus coat protein VP4 superfamily / 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. / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsFairhead, M. / Lithgo, R.M. / MacLean, E.M. / Bowesman-Jones, H. / Aschenbrenner, J.C. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Godoy, A.S. / Marples, P.G. ...Fairhead, M. / Lithgo, R.M. / MacLean, E.M. / Bowesman-Jones, H. / Aschenbrenner, J.C. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Godoy, A.S. / Marples, P.G. / Fearon, D. / von Delft, F. / Koekemoer, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171399 United States
CitationJournal: To Be Published
Title: Coxsackievirus B3 3C protease in C121 spacegroup
Authors: Fairhead, M. / Lithgo, R.M. / MacLean, E.M. / Bowesman-Jones, H. / Aschenbrenner, J.C. / Balcomb, B.H. / Capkin, E. / Chandran, A.V. / Godoy, A.S. / Marples, P.G. / Fearon, D. / von Delft, F. / Koekemoer, L.
History
DepositionJun 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)20,2861
Polymers20,2861
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8740 Å2
Unit cell
Length a, b, c (Å)78.503, 64.871, 39.43
Angle α, β, γ (deg.)90, 115.874, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

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Components

#1: Protein Genome polyprotein


Mass: 20286.279 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: E3SVR4, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ShotGun1 Eco 0.2 Magnesium chloride hexahydrate 0.1 M Tris, pH 8.5 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.34→47.78 Å / Num. obs: 26456 / % possible obs: 66.32 % / Redundancy: 5.6 % / CC1/2: 0.992 / Net I/σ(I): 29.2
Reflection shellResolution: 1.34→1.36 Å / Num. unique obs: 100 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→47.778 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.211 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2029 1314 4.967 %
Rwork0.1545 25142 -
all0.157 --
obs-26456 66.317 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.327 Å2
Baniso -1Baniso -2Baniso -3
1--1.466 Å20 Å20.191 Å2
2---0.112 Å20 Å2
3---0.947 Å2
Refinement stepCycle: LAST / Resolution: 1.34→47.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 0 121 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121482
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161437
X-RAY DIFFRACTIONr_angle_refined_deg2.1991.8372012
X-RAY DIFFRACTIONr_angle_other_deg0.8941.7483305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2255192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66710260
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.6621064
X-RAY DIFFRACTIONr_chiral_restr0.1230.2223
X-RAY DIFFRACTIONr_chiral_restr_other0.0160.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021764
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02342
X-RAY DIFFRACTIONr_nbd_refined0.2120.2235
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.21166
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2665
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.25
X-RAY DIFFRACTIONr_nbd_other0.1550.249
X-RAY DIFFRACTIONr_mcbond_it9.0342.122750
X-RAY DIFFRACTIONr_mcbond_other9.0262.122750
X-RAY DIFFRACTIONr_mcangle_it12.4723.831948
X-RAY DIFFRACTIONr_mcangle_other12.4743.834949
X-RAY DIFFRACTIONr_scbond_it11.5852.565732
X-RAY DIFFRACTIONr_scbond_other11.5782.57733
X-RAY DIFFRACTIONr_scangle_it15.8914.5311064
X-RAY DIFFRACTIONr_scangle_other15.8844.5351065
X-RAY DIFFRACTIONr_lrange_it19.7320.6651524
X-RAY DIFFRACTIONr_lrange_other19.59220.5891510
X-RAY DIFFRACTIONr_rigid_bond_restr5.9932919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.34-1.3750.39940.3112020.31329540.6130.9336.97360.315
1.375-1.4130.33180.2943920.29628440.9270.94614.41630.296
1.413-1.4540.275300.2585920.25927960.9460.96222.24610.252
1.454-1.4990.236370.2047430.20526840.9710.9829.06110.188
1.499-1.5480.205510.1829700.18326440.9670.98538.61570.161
1.548-1.6020.204630.15612300.15825320.9790.98951.06640.127
1.602-1.6620.227900.13316020.13824320.9730.99169.57240.105
1.662-1.730.211790.12420620.12823570.9770.99290.83580.097
1.73-1.8070.183950.12620940.12822760.9810.99296.17750.101
1.807-1.8950.1981240.12319900.12721680.9790.99297.50920.101
1.895-1.9970.2970.12419000.12820480.9760.99297.50980.105
1.997-2.1180.1861070.13718210.1419690.9780.9997.91770.121
2.118-2.2640.2311080.13816540.14417960.9670.98998.10690.127
2.264-2.4450.209920.15316120.15617310.9710.98698.44020.141
2.445-2.6780.239690.16514870.16815770.970.98398.66840.155
2.678-2.9930.242720.17513510.17814410.960.9898.75090.172
2.993-3.4530.206640.16311730.16512490.9710.98499.03920.167
3.453-4.2240.176600.15510070.15710740.980.98399.34820.171
4.224-5.950.162380.1477960.1488380.9880.98999.52270.171
5.95-47.7780.19160.2194640.2194830.9740.96599.37890.251

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