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- PDB-5nfs: Structure of coxsackievirus B3 3C protease in complex with the al... -

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Basic information

Entry
Database: PDB / ID: 5nfs
TitleStructure of coxsackievirus B3 3C protease in complex with the alpha-ketoamide (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide (cinnamoyl-phenylalanine-GlnLactam-CO-CO-NH-benzyl)
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Viral protease / enterovirus / alpha-ketoamide / inhibitor
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 / channel activity / monoatomic ion transmembrane transport / 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 / host cell nucleus / 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 / 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
Chem-D03 / Genome polyprotein
Similarity search - Component
Biological speciesCoxsackievirus B3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMa, Q. / Zhang, L. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Center for Infection Research (DZIF)TTU 01.803 Germany
CitationJournal: To Be Published
Title: Alpha-ketoamides as broad-spectrum inhibitors of coronavirus and enterovirus replication
Authors: Lin, D. / Zhang, L. / Kusov, Y. / Nian, Y. / Ma, Q. / Wang, J. / Leyssen, P. / Lanko, K. / Neyts, J. / de Wilde, A. / Snijder, E.J. / Liu, H. / Hilgenfeld, R.
History
DepositionMar 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9982
Polymers20,4291
Non-polymers5691
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.657, 64.354, 39.477
Angle α, β, γ (deg.)90.00, 115.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Genome polyprotein


Mass: 20429.488 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: Q5UEA2
#2: Chemical ChemComp-D03 / (S)-N-benzyl-3-((S)-2-cinnamamido-3-phenylpropanamido)-2-oxo-4-((S)-2-oxopyrrolidin-3-yl)butanamide


Mass: 568.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M MgCl2, pH 8.5, and PEG 3350 varied from 22% to 27%
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→47.41 Å / Num. obs: 16209 / % possible obs: 99.4 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.023 / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.393 / Num. unique obs: 2332 / CC1/2: 0.887 / Rpim(I) all: 0.265 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ccoxsackievirus B3 3C protease

Resolution: 1.8→47.41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.786 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23933 828 5.1 %RANDOM
Rwork0.17867 ---
obs0.1817 15381 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.438 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å21.94 Å2
2---2.76 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 42 106 1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191473
X-RAY DIFFRACTIONr_bond_other_d0.0020.021379
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9971984
X-RAY DIFFRACTIONr_angle_other_deg1.0333.0013195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98824.12763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60215249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.652158
X-RAY DIFFRACTIONr_chiral_restr0.1110.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211633
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6772.788719
X-RAY DIFFRACTIONr_mcbond_other1.6642.786718
X-RAY DIFFRACTIONr_mcangle_it2.3454.175897
X-RAY DIFFRACTIONr_mcangle_other2.3434.176898
X-RAY DIFFRACTIONr_scbond_it2.2983.268752
X-RAY DIFFRACTIONr_scbond_other2.2973.277753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4614.7821087
X-RAY DIFFRACTIONr_long_range_B_refined6.40134.1431531
X-RAY DIFFRACTIONr_long_range_B_other6.39934.1661532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 65 -
Rwork0.267 1101 -
obs--98.81 %
Refinement TLS params.Method: refined / Origin x: -16.5333 Å / Origin y: -0.0584 Å / Origin z: -1.0135 Å
111213212223313233
T0.0075 Å2-0.0004 Å20.0078 Å2-0.0247 Å2-0.0062 Å2--0.0204 Å2
L3.7831 °20.5048 °2-0.7373 °2-5.0549 °2-1.1851 °2--3.0908 °2
S0.1016 Å °0.0748 Å °0.1607 Å °-0.0245 Å °-0.0424 Å °0.2097 Å °-0.0425 Å °-0.2124 Å °-0.0592 Å °

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