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- PDB-3q3x: Crystal structure of the main protease (3C) from human enteroviru... -

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Basic information

Entry
Database: PDB / ID: 3q3x
TitleCrystal structure of the main protease (3C) from human enterovirus B EV93
ComponentsHEVB EV93 3C protease
KeywordsHYDROLASE / cysteine trypsin-like protease / 3C cysteine protease (picornain 3C)
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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / 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) / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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
Biological speciesHuman enterovirus B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsCostenaro, L. / Sola, M. / Coutard, B. / Norder, H. / Canard, B. / Coll, M.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Basis for Antiviral Inhibition of the Main Protease, 3C, from Human Enterovirus 93.
Authors: Costenaro, L. / Kaczmarska, Z. / Arnan, C. / Janowski, R. / Coutard, B. / Sola, M. / Gorbalenya, A.E. / Norder, H. / Canard, B. / Coll, M.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEVB EV93 3C protease
B: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,48810
Polymers42,8872
Non-polymers6018
Water6,107339
1
A: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7204
Polymers21,4441
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEVB EV93 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7686
Polymers21,4441
Non-polymers3255
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.072, 65.216, 66.355
Angle α, β, γ (deg.)90.000, 90.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEVB EV93 3C protease


Mass: 21443.510 Da / Num. of mol.: 2 / Mutation: M139V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human enterovirus B / Gene: 3C / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5DSM6, picornain 3C
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS MAY BE A NATURAL VARIANT.

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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: 1.97 Å3/Da / Density % sol: 37.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 8K, 0.1M cacodylate, 0.2M magnesium acetate, cryo + 20% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2007 / Details: mirrors
RadiationMonochromator: horizontally side diffracting Silicon 111 crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.9→66.37 Å / Num. all: 26356 / Num. obs: 26356 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.10.4121.61183738280.412100
2-2.123.10.2882.51121936220.288100
2.12-2.2740.2692.51371134020.269100
2.27-2.455.20.2193.31655931920.219100
2.45-2.695.20.18341516329080.183100
2.69-35.20.1451388526780.14100
3-3.475.20.1026.51218623400.102100
3.47-4.255.20.07681034319930.07699.8
4.25-6.015.20.05410.6791015330.05499.5
6.01-46.52450.04812.443048600.04898.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å39.07 Å
Translation1.9 Å39.07 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASER1.3phasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L1N

1l1n


Resolution: 1.9→46.524 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 1334 5.1 %RANDOM
Rwork0.1484 ---
all0.1514 26318 --
obs0.1514 26318 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.5 Å2 / Biso mean: 14.4357 Å2 / Biso min: 4.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2847 0 38 339 3224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223158
X-RAY DIFFRACTIONr_bond_other_d00.022940
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9694294
X-RAY DIFFRACTIONr_angle_other_deg10.40536863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70223.399153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.751528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213550
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02672
X-RAY DIFFRACTIONr_mcbond_it0.7441.51889
X-RAY DIFFRACTIONr_mcbond_other01.5788
X-RAY DIFFRACTIONr_mcangle_it1.36923064
X-RAY DIFFRACTIONr_scbond_it2.17131269
X-RAY DIFFRACTIONr_scangle_it3.5184.51200
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 84 -
Rwork0.176 1871 -
all-1955 -
obs--100 %

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