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- PDB-7p35: Structure of the SARS-CoV-2 3CL protease in complex with rupintrivir -

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Basic information

Entry
Database: PDB / ID: 7p35
TitleStructure of the SARS-CoV-2 3CL protease in complex with rupintrivir
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Protease / Inhibitor / SARS-CoV-2
Function / homology
Function and homology information


SARS coronavirus main proteinase / DNA helicase / ubiquitinyl hydrolase 1 / RNA helicase / RNA-directed RNA polymerase
Similarity search - Function
Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation ...Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Macro domain / Macro domain profile. / Macro domain-like / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-AG7 / 3C-like proteinase
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.256 Å
AuthorsFabrega-Ferrer, M. / Perez-Saavedra, J. / Herrera-Morande, A. / Coll, M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBFU2017-83720-P Spain
Spanish National Research CouncilAEPP2020 Spain
CitationJournal: Antiviral Res. / Year: 2022
Title: Structure and inhibition of SARS-CoV-1 and SARS-CoV-2 main proteases by oral antiviral compound AG7404.
Authors: Fabrega-Ferrer, M. / Herrera-Morande, A. / Muriel-Goni, S. / Perez-Saavedra, J. / Bueno, P. / Castro, V. / Garaigorta, U. / Gastaminza, P. / Coll, M.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / citation_author / database_2 / pdbx_database_related
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: 3C-like proteinase
BBB: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8524
Polymers67,6512
Non-polymers1,2012
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-26 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.023, 54.024, 114.067
Angle α, β, γ (deg.)90.000, 100.774, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3C-like proteinase / Growth factor-like peptide / Guanine-N7 methyltransferase / Helicase / Host translation inhibitor ...Growth factor-like peptide / Guanine-N7 methyltransferase / Helicase / Host translation inhibitor nsp1 / Leader protein / NendoU / Non-structural protein 10 / Non-structural protein 2 / Non-structural protein 3 / Non-structural protein 4 / Non-structural protein 6 / Non-structural protein 7 / Non-structural protein 8 / Non-structural protein 9 / ORF1ab polyprotein / Papain-like proteinase / RNA-directed RNA polymerase / Replicase polyprotein 1ab / Uridylate-specific endoribonuclease / p65 homolog


Mass: 33825.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: ORF1ab / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7L9RWV7, RNA-directed RNA polymerase, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, DNA helicase, RNA helicase
#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: isolated from a natural source / Formula: C31H41FN4O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: antivirus, protease inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Triammonium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.256→56.091 Å / Num. obs: 21599 / % possible obs: 84.4 % / Redundancy: 2.5 % / CC1/2: 0.998 / Net I/σ(I): 9.6
Reflection shellResolution: 2.256→2.295 Å / Num. unique obs: 1085 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SARS-CoV-2 3CL protease

Resolution: 2.256→56.091 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.11 / SU ML: 0.233 / Cross valid method: FREE R-VALUE / ESU R: 0.963 / ESU R Free: 0.304
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2581 1115 5.162 %
Rwork0.2 20484 -
all0.203 --
obs-21599 84.388 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.928 Å2
Baniso -1Baniso -2Baniso -3
1-0.047 Å2-0 Å20.022 Å2
2---0.034 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.256→56.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 86 34 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134890
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174538
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.646644
X-RAY DIFFRACTIONr_angle_other_deg1.2221.57510424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1175606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34322.869244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10315770
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg17.903152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4951522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021154
X-RAY DIFFRACTIONr_nbd_refined0.2040.2908
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.24277
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22372
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22271
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2116
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.222
X-RAY DIFFRACTIONr_nbd_other0.2120.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.180.21
X-RAY DIFFRACTIONr_mcbond_it3.6435.22430
X-RAY DIFFRACTIONr_mcbond_other3.6385.1982429
X-RAY DIFFRACTIONr_mcangle_it5.5117.7943034
X-RAY DIFFRACTIONr_mcangle_other5.5117.7953035
X-RAY DIFFRACTIONr_scbond_it4.065.6562460
X-RAY DIFFRACTIONr_scbond_other4.0595.6582461
X-RAY DIFFRACTIONr_scangle_it6.2158.3273610
X-RAY DIFFRACTIONr_scangle_other6.2148.333611
X-RAY DIFFRACTIONr_lrange_it9.86861.7665172
X-RAY DIFFRACTIONr_lrange_other9.86761.7785173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.256-2.3150.352830.3161527X-RAY DIFFRACTION87.8342
2.315-2.3780.353790.31534X-RAY DIFFRACTION87.048
2.378-2.4470.262680.2711478X-RAY DIFFRACTION87.4929
2.447-2.5230.302630.2691414X-RAY DIFFRACTION85.2771
2.523-2.6050.36740.2611381X-RAY DIFFRACTION86.0438
2.605-2.6970.332940.2521286X-RAY DIFFRACTION84.8708
2.697-2.7980.346750.2321254X-RAY DIFFRACTION84.4882
2.798-2.9120.373680.2141223X-RAY DIFFRACTION86.4702
2.912-3.0420.24560.1871180X-RAY DIFFRACTION85.1826
3.042-3.190.276720.1881137X-RAY DIFFRACTION85.3814
3.19-3.3630.223650.1751042X-RAY DIFFRACTION84.5684
3.363-3.5660.195510.169984X-RAY DIFFRACTION83.1994
3.566-3.8120.253480.183934X-RAY DIFFRACTION82.7993
3.812-4.1170.23330.201863X-RAY DIFFRACTION80.7935
4.117-4.510.201380.162798X-RAY DIFFRACTION81.9608
4.51-5.0410.24380.172708X-RAY DIFFRACTION80.9989
5.041-5.8190.331300.217627X-RAY DIFFRACTION80.8118
5.819-7.1220.172280.187519X-RAY DIFFRACTION79.6215
7.122-10.0520.23300.148385X-RAY DIFFRACTION75.4545
10.052-56.0910.221220.188210X-RAY DIFFRACTION72.5

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