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- PDB-2zu3: Complex structure of CVB3 3C protease with TG-0204998 -

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Basic information

Entry
Database: PDB / ID: 2zu3
TitleComplex structure of CVB3 3C protease with TG-0204998
Components3C proteinase
Keywordshydrolase/hydrolase inhibitor / protease-inhibitor complex / Hydrolase / Thiol protease / hydrolase-hydrolase 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 / host cell cytoplasm / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont 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 / nucleotide binding / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
TG-0204998 / Chem-ZU3 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman coxsackievirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLee, C.C. / Tsui, Y.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 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Structure summary
Revision 1.3Apr 16, 2014Group: Refinement description
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9142
Polymers20,2981
Non-polymers6161
Water3,585199
1


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

A: 3C proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8284
Polymers40,5972
Non-polymers1,2322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.800, 64.620, 39.520
Angle α, β, γ (deg.)90.00, 115.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

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Components

#1: Protein 3C proteinase


Mass: 20298.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coxsackievirus / Strain: B3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli)
References: UniProt: Q90092, UniProt: P03313*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ZU3 / N-[(benzyloxy)carbonyl]-3-[(2,2-dimethylpropanoyl)amino]-L-alanyl-N-[(1R)-4-oxo-1-{[(3S)-2-oxopyrrolidin-3-yl]methyl}pentyl]-L-leucinamide / TG-0204998


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 615.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H49N5O7 / References: TG-0204998
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP ...THE UNBOUND VERSION OF THE INHIBITOR HAS A DOUBLE BOND BETWEEN ATOMS C63 AND C82, WHICH OPENS UP WHEN IT COVALENTLY BINDS TO CYS 147 OF THE ENZYME

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 24~30% PEG 4000, 0.2M magnesium chloride, 0.1M Tris-HCl , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 17634 / Num. obs: 17369 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.6
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2 / Num. unique all: 1718

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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: 1.75→25.03 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
Rfree0.219 793 4.5 %RANDOM
Rwork0.192 ---
obs0.192 16266 92.5 %-
all-17582 --
Solvent computationBsol: 86.849 Å2
Displacement parametersBiso max: 82.47 Å2 / Biso mean: 34.23 Å2 / Biso min: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.055 Å20 Å2-6.482 Å2
2--8.522 Å20 Å2
3----8.577 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 44 199 1641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.193

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