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- PDB-9dcf: Structure of Coxsackievirus B3 cloverleaf RNA in complex with 3Cp... -

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Basic information

Entry
Database: PDB / ID: 9dcf
TitleStructure of Coxsackievirus B3 cloverleaf RNA in complex with 3Cpro dimer
Components
  • Protease 3C
  • cloverleaf RNA
KeywordsRNA BINDING PROTEIN/RNA / enterovirus 3Cpro / cloverleaf RNA / coxsackievirus / protein-RNA complex / RNA BINDING PROTEIN-RNA 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
Picornavirus coat protein VP4 superfamily / 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 superfamily / 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 / 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
RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsGottipati, K. / Dias, D.S.A.N. / Choi, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI157336 United States
CitationJournal: Sci Adv / Year: 2025
Title: Structure of coxsackievirus cloverleaf RNA and 3C pro dimer establishes the RNA-binding mechanism of enterovirus protease 3C pro.
Authors: Dias-Solange, D. / Le, M.T. / Gottipati, K. / Choi, K.H.
History
DepositionAug 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease 3C
B: Protease 3C
C: cloverleaf RNA


Theoretical massNumber of molelcules
Total (without water)71,7243
Polymers71,7243
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-26 kcal/mol
Surface area27980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.018, 200.821, 71.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Protease 3C / Picornain 3C / P3C


Mass: 21467.592 Da / Num. of mol.: 2 / Fragment: UNP residues 1541-1723 / Mutation: C147A,G55A,D58A,V63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Nancy) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03313, picornain 3C
#2: RNA chain cloverleaf RNA


Mass: 28789.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxsackievirus B3 (strain Nancy) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 8% v/v Tacsimate, pH 6.0, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.87→48.93 Å / Num. obs: 29950 / % possible obs: 98.8 % / Redundancy: 11 % / CC1/2: 0.947 / Rpim(I) all: 0.098 / Rrim(I) all: 0.337 / Net I/σ(I): 5
Reflection shellResolution: 2.87→2.95 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 1384 / CC1/2: 0.661 / Rpim(I) all: 0.833

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.21.1_5286phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→48.93 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 31.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 1534 6.74 %
Rwork0.2369 --
obs0.2394 22756 74.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 1627 0 12 4410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094641
X-RAY DIFFRACTIONf_angle_d1.2826633
X-RAY DIFFRACTIONf_dihedral_angle_d14.9261300
X-RAY DIFFRACTIONf_chiral_restr0.056806
X-RAY DIFFRACTIONf_plane_restr0.011570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.970.3342640.3167878X-RAY DIFFRACTION34
2.97-3.070.3471830.28531243X-RAY DIFFRACTION49
3.07-3.20.3231050.2841512X-RAY DIFFRACTION59
3.2-3.340.33991360.26571761X-RAY DIFFRACTION70
3.34-3.520.36271480.25941953X-RAY DIFFRACTION76
3.52-3.740.28771520.25082097X-RAY DIFFRACTION82
3.74-4.030.28441400.22781986X-RAY DIFFRACTION78
4.03-4.430.21791640.19742209X-RAY DIFFRACTION85
4.43-5.070.22781690.18912368X-RAY DIFFRACTION91
5.07-6.390.25711820.23662509X-RAY DIFFRACTION95
6.39-48.930.25841910.24832706X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8774-2.0186-0.25244.0517-0.74633.4571-0.261-0.16050.02460.19630.2141-0.25750.06910.6466-0.05690.2190.1005-0.01010.8775-0.06950.164416.299847.030652.5513
20.63380.1697-0.14661.5589-0.18255.52280.1805-0.32210.08120.1638-0.2217-0.364-0.19530.93020.12590.2480.1141-0.08391.15360.13290.101312.058549.260957.871
33.96691.10741.695.7608-2.19372.50010.1160.22271.28651.41740.2702-1.1844-1.6348-1.0483-0.38881.98040.85650.44671.4129-0.09392.494636.515922.802648.463
45.404-0.67582.01920.9662-1.10231.63960.08491.36-1.3719-0.2379-0.0160.23820.2081-0.3814-0.10851.38610.23160.22651.3472-0.08451.126716.06046.705946.0751
53.7928-0.69421.6282.14561.09281.728-0.36330.0385-0.94380.3662-0.12190.33810.6045-0.5009-0.26250.2397-0.00360.02141.18610.08570.38479.300531.642735.4826
62.35851.3432-1.24015.5988-2.00261.0255-0.73590.4696-0.3270.80850.8423-2.1246-0.6275-0.5463-0.0681.21320.4233-0.04631.77540.06351.489442.121221.682653.1912
72.6309-0.5603-1.10041.53870.18992.38310.44850.37940.05940.1024-0.2696-0.2137-0.32940.4582-0.06860.3474-0.1458-0.0030.88750.01840.117317.660847.534524.5001
82.34230.07360.88231.00921.60532.8176-0.23140.16930.05910.03580.0459-0.06140.02610.70780.17750.229-0.03480.05091.1185-0.08990.287428.434544.339422.1337
91.47510.0131-0.8061.8494-0.46110.93030.0105-0.10430.08680.23720.19060.101-0.09150.1348-0.20280.23490.13920.06451.1516-0.09470.206131.813840.4723.238
104.8925-0.0672-1.47982.6638-0.21421.1530.47820.2738-0.3035-0.2355-0.35820.1590.24030.2731-0.01560.11840.0113-0.02380.7608-0.01490.325722.588338.939216.9603
115.30982.14270.65424.7798-3.07943.59530.25030.61530.0237-0.0630.41640.44410.06260.1134-0.57160.20060.1332-0.00230.9646-0.17820.33287.753544.97338.7521
120.4329-0.624-1.27232.1588-0.15336.90470.15780.30840.0766-0.03180.30110.0705-0.61390.1619-0.32510.30220.17480.00810.70590.02260.12513.05855.163818.4258
130.3487-0.17750.17440.0908-0.05091.05490.0137-0.05410.0143-0.01240.0144-0.0463-0.15760.320.40680.2871-0.255-0.1191.28190.32570.382223.997151.62642.1802
143.6450.49974.39910.32880.50255.3446-0.5565-1.24180.5320.04990.31860.1647-1.0853-1.04170.62990.35420.272-0.12561.37290.05590.277816.176757.778813.415
154.47381.60140.75353.05210.75672.4694-0.07910.24970.2073-0.0246-0.11350.17050.48850.10690.1870.2746-0.2171-0.11790.42350.06250.084912.235548.193415.7213
160.1143-0.20840.40021.55320.32215.38450.04790.1030.0005-0.19220.0199-0.0608-0.31470.07030.06040.2809-0.2522-0.01841.2155-0.23070.11417.126947.526110.1258
171.8587-0.28850.21870.66990.05240.6508-0.1678-0.17890.34160.05190.1339-0.13640.1005-0.1639-0.1374-0.3374-0.1749-0.04091.06050.00620.25315.19852.208447.4675
185.8333-1.7398-1.3111.64460.84070.9597-0.0286-0.3224-0.0566-0.33060.41430.15410.2795-0.5759-0.20830.2675-0.16040.02950.75460.01760.18283.379941.67942.7539
191.7011-0.17881.36060.66420.111.6954-0.0392-0.056-0.0380.12340.1372-0.01880.0783-0.5178-0.04670.1006-0.002-0.17491.34380.14560.256919.411448.757452.6296
202.08870.11120.69950.43020.21061.4426-0.1167-0.02380.15890.06430.10670.0665-0.1932-0.34340.20650.23510.2774-0.11441.28920.09840.318212.788155.582264.2415
211.3919-1.43060.14031.4723-0.14560.01460.1969-0.03650.42630.01240.0362-0.5772-0.1511.2691-0.21630.4567-0.05920.10432.0719-0.15220.488720.954157.586152.1828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 150 through 164 )
2X-RAY DIFFRACTION2chain 'B' and (resid 165 through 180 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 9 )
4X-RAY DIFFRACTION4chain 'C' and (resid 10 through 45 )
5X-RAY DIFFRACTION5chain 'C' and (resid 46 through 80 )
6X-RAY DIFFRACTION6chain 'C' and (resid 81 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 31 )
8X-RAY DIFFRACTION8chain 'A' and (resid 32 through 51 )
9X-RAY DIFFRACTION9chain 'A' and (resid 52 through 61 )
10X-RAY DIFFRACTION10chain 'A' and (resid 62 through 89 )
11X-RAY DIFFRACTION11chain 'A' and (resid 90 through 99 )
12X-RAY DIFFRACTION12chain 'A' and (resid 100 through 123 )
13X-RAY DIFFRACTION13chain 'A' and (resid 124 through 134 )
14X-RAY DIFFRACTION14chain 'A' and (resid 135 through 149 )
15X-RAY DIFFRACTION15chain 'A' and (resid 150 through 163 )
16X-RAY DIFFRACTION16chain 'A' and (resid 164 through 180 )
17X-RAY DIFFRACTION17chain 'B' and (resid 2 through 77 )
18X-RAY DIFFRACTION18chain 'B' and (resid 78 through 89 )
19X-RAY DIFFRACTION19chain 'B' and (resid 90 through 123 )
20X-RAY DIFFRACTION20chain 'B' and (resid 124 through 138 )
21X-RAY DIFFRACTION21chain 'B' and (resid 139 through 149 )

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