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- PDB-3ruo: Complex structure of HevB EV93 main protease 3C with Rupintrivir ... -

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Basic information

Entry
Database: PDB / ID: 3ruo
TitleComplex structure of HevB EV93 main protease 3C with Rupintrivir (AG7088)
ComponentsHEVB EV93 3C PROTEASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE TRYPSIN-LIKE PROTEASE / 3C CYSTEINE PROTEASE (PICORNAIN 3C) / RUPINTRIVIR (AG7088) / COVALENTLY BOUND INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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-AG7 / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKaczmarska, Z. / Janowski, R. / Costenaro, L. / 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
DepositionMay 5, 2011Deposition 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 1.3Nov 20, 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

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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)44,0767
Polymers42,7912
Non-polymers1,2855
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-39 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.995, 63.911, 66.357
Angle α, β, γ (deg.)90.00, 90.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEVB EV93 3C PROTEASE


Mass: 21395.512 Da / Num. of mol.: 2
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-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Comment: antivirus, protease inhibitor*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.25 M MgCl2, 0.1 M Tris, 25% PEG 8k, pH 8.5, VAPOR DIFFUSION, SITTING 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 2, 2011 / 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: 1.5→30 Å / Num. obs: 52513 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.5→1.55 Å / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Q3Y

3q3y


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.851 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19796 2658 5.1 %RANDOM
Rwork0.16581 ---
all0.16745 49523 --
obs0.16745 49523 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20.07 Å2
2--0.72 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 89 376 3307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223203
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9964366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9055418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19623.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82815552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1931521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212481
X-RAY DIFFRACTIONr_mcbond_it0.5281.51902
X-RAY DIFFRACTIONr_mcangle_it1.0282.53085
X-RAY DIFFRACTIONr_scbond_it2.32551301
X-RAY DIFFRACTIONr_scangle_it3.733101253
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.256 394 -
Rwork0.223 7138 -
obs--99.97 %
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)
10.6222-0.417-0.34660.97960.05460.89460.0257-0.08740-0.03460.0166-0.1196-0.02250.0586-0.04230.0154-0.00950.00040.02360.00260.0339-11.150610.8671-0.9255
23.5771-1.02540.06330.95790.81071.2408-0.1251-0.4007-0.01620.12710.08530.00360.1098-0.04520.03980.03590.00460.01030.05430.02310.0416-17.34876.76226.5499
35.9826-2.60112.2892.4323-0.92662.4153-0.0884-0.15380.12170.10480.1041-0.1784-0.21580.1632-0.01570.0389-0.0265-0.00410.0475-0.030.0373-12.723820.44936.1825
41.0593-0.157-0.23620.8559-0.0820.90420.03410.0406-0.0101-0.0698-0.01880.0369-0.0085-0.0763-0.01520.0244-0.0031-0.00440.0108-0.00420.0165-22.037914.5074-7.9087
51.29050.57940.11981.0010.32292.03140.03360.10920.02950.107-0.00010.1233-0.080.001-0.03350.033-0.00260.00470.01680.00440.0489-8.016517.8945-31.7513
61.42940.3570.09730.7569-0.50930.7765-0.03810.311-0.0292-0.06260.04240.00730.03310.0372-0.00430.0159-0.0050.0040.0907-0.03070.0211-3.363413.3948-42.0157
7-0.09110.1285-0.22431.21541.12361.3451-0.0080.12280.2148-0.0867-0.05870.3285-0.2798-0.11430.06660.1722-0.0195-0.02490.1020.07980.2368-7.260527.4642-36.8663
81.68980.1663-0.3130.71220.1391.55770.0356-0.0463-0.02350.0617-0.0135-0.0379-0.00330.1484-0.02210.032-0.006-0.00320.0143-0.00180.01862.448617.677-25.2821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 48
2X-RAY DIFFRACTION2A49 - 78
3X-RAY DIFFRACTION3A79 - 93
4X-RAY DIFFRACTION4A94 - 182
5X-RAY DIFFRACTION5B0 - 40
6X-RAY DIFFRACTION6B41 - 78
7X-RAY DIFFRACTION7B79 - 93
8X-RAY DIFFRACTION8B94 - 180

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