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- PDB-9fsb: Coxsackievirus B3 3C protease in P121 spacegroup -

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Basic information

Entry
Database: PDB / ID: 9fsb
TitleCoxsackievirus B3 3C protease in P121 spacegroup
ComponentsGenome polyprotein
KeywordsHYDROLASE / B clade 3C protease enterovirus
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 / symbiont-mediated suppression of host gene expression ...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 / symbiont-mediated suppression of host gene expression / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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: 1.592 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 P121 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 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)40,5732
Polymers40,5732
Non-polymers00
Water88349
1
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)20,2861
Polymers20,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)20,2861
Polymers20,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.485, 45.967, 66.884
Angle α, β, γ (deg.)90, 101.559, 90
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 180 / Label seq-ID: 1 - 180

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Genome polyprotein


Mass: 20286.279 Da / Num. of mol.: 2
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.: 49 / 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: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Shotgun1 A01 0.1 M Magnesium chloride, 0.1 M TRIS pH 8.2, 25% PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.59→50.441 Å / Num. obs: 33816 / % possible obs: 81.74 % / Redundancy: 6 % / CC1/2: 0.993 / Net I/σ(I): 4.6
Reflection shellResolution: 1.59→1.62 Å / Num. unique obs: 1991 / CC1/2: 0.392

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.592→50.441 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.884 / SU B: 17.573 / SU ML: 0.241 / Cross valid method: FREE R-VALUE / ESU R: 0.605 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3008 1384 4.918 %
Rwork0.2095 26759 -
all0.214 --
obs-28143 68.102 %
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: 35.562 Å2
Baniso -1Baniso -2Baniso -3
1--3.632 Å2-0 Å21.426 Å2
2--5.924 Å20 Å2
3----2.653 Å2
Refinement stepCycle: LAST / Resolution: 1.592→50.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 0 49 2845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0122854
X-RAY DIFFRACTIONr_bond_other_d0.0060.0162756
X-RAY DIFFRACTIONr_angle_refined_deg2.5851.8423852
X-RAY DIFFRACTIONr_angle_other_deg1.2271.7526344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5915358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.096514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08810500
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.49310124
X-RAY DIFFRACTIONr_chiral_restr0.1410.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023336
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02652
X-RAY DIFFRACTIONr_nbd_refined0.1920.2451
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.22604
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21324
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.251
X-RAY DIFFRACTIONr_nbd_other0.1550.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2470.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0810.21
X-RAY DIFFRACTIONr_mcbond_it14.5333.2821438
X-RAY DIFFRACTIONr_mcbond_other14.4983.2811438
X-RAY DIFFRACTIONr_mcangle_it19.4515.9241794
X-RAY DIFFRACTIONr_mcangle_other19.4625.9261795
X-RAY DIFFRACTIONr_scbond_it16.6493.751416
X-RAY DIFFRACTIONr_scbond_other16.6453.7531417
X-RAY DIFFRACTIONr_scangle_it22.2966.7292058
X-RAY DIFFRACTIONr_scangle_other22.2916.7322059
X-RAY DIFFRACTIONr_lrange_it26.14637.7522963
X-RAY DIFFRACTIONr_lrange_other26.1537.7692959
X-RAY DIFFRACTIONr_rigid_bond_restr11.63735610
X-RAY DIFFRACTIONr_ncsr_local_group_10.1880.054922
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.188210.05006
12AX-RAY DIFFRACTIONLocal ncs0.188210.05006
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
1.592-1.6330.46430.291190.32430130.9180.960.73020.264
1.633-1.6780.38550.374320.37529450.9140.9121.25640.356
1.678-1.7260.41170.4353590.43428980.9610.92112.97450.411
1.726-1.7790.423370.3735560.37627940.8870.91521.22410.36
1.779-1.8380.345490.3729840.37127090.9420.93438.13220.362
1.838-1.9020.414940.35317680.35626050.9140.9571.47790.341
1.902-1.9740.321230.32223660.32225390.9380.95598.03070.311
1.974-2.0540.3351250.27523140.27824390.9360.9741000.253
2.054-2.1450.331990.25322490.25723500.9580.97899.91490.222
2.145-2.250.3191040.23621270.2422310.8980.981000.201
2.25-2.3710.2911070.24220210.24521280.9270.9771000.201
2.371-2.5150.336940.22919260.23420200.930.9761000.188
2.515-2.6880.285920.20818170.21119090.9490.981000.166
2.688-2.9030.343890.1816950.18817840.9060.9841000.143
2.903-3.1790.291860.17515360.18216220.9540.9841000.141
3.179-3.5520.301860.16114090.16814950.9430.9851000.14
3.552-4.0980.261530.17111950.17513060.960.98395.5590.152
4.098-5.0110.243580.1510530.15511300.9510.98698.31860.14
5.011-7.0520.279390.2048400.2078800.9670.97399.88640.194
7.052-50.4410.349240.2254930.235190.8650.95699.61460.23

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