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- PDB-2zty: crystal structure of 3C protease from CVB3 in space group C2 -

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Basic information

Entry
Database: PDB / ID: 2zty
Titlecrystal structure of 3C protease from CVB3 in space group C2
Components3C proteinasePicornain 3C
KeywordsHYDROLASE / protease / Thiol protease
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 MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 MDA-5 activity / 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-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / host cell cytoplasm / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / nucleotide binding / 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 / cytoplasm
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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLee, C.C. / Wang, A.H.-J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural Basis of Inhibition Specificities of 3C and 3C-like Proteases by Zinc-coordinating and Peptidomimetic Compounds
Authors: Lee, C.C. / Kuo, C.J. / Ko, T.P. / Hsu, M.F. / Tsui, Y.C. / Chang, S.C. / Yang, S. / Chen, S.J. / Chen, H.C. / Hsu, M.C. / Shih, S.R. / Liang, P.H. / Wang, A.H.-J.
History
DepositionOct 10, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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

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Assembly

Deposited unit
A: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)20,2981
Polymers20,2981
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 3C proteinase

A: 3C proteinase


Theoretical massNumber of molelcules
Total (without water)40,5972
Polymers40,5972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1500 Å2
ΔGint-16 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.78, 64.43, 40.31
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-248-

HOH

21A-345-

HOH

31A-359-

HOH

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Components

#1: Protein 3C proteinase / Picornain 3C


Mass: 20298.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus B3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli)
References: UniProt: Q90092, UniProt: P03313*PLUS, picornain 3C
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.72→30 Å / Num. all: 18698 / Num. obs: 17969 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 44.7
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1511

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZTX

2ztx


Resolution: 1.72→25.3 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 842 -RANDOM
Rwork0.236 ---
all0.238 18615 --
obs0.238 17459 93.8 %-
Displacement parametersBiso max: 92.15 Å2 / Biso mean: 43.615 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 0 234 1603

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