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- PDB-7p51: CRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH ... -

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Basic information

Entry
Database: PDB / ID: 7p51
TitleCRYSTAL STRUCTURE OF THE SARS-COV-2 MAIN PROTEASE COMPLEXED WITH FRAGMENT F01
Components3C-like proteinase
KeywordsVIRAL PROTEIN / 3CLPRO / MAIN PROTEASE / SARS-COV-2 / 2019-NCOV / INHIBITOR
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N 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 / Carbamoyl-phosphate synthase subdomain signature 2. ...Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / 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 / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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 replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-5P9 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.474 Å
AuthorsHanoulle, X. / Moschidi, D.
Funding support France, 1items
OrganizationGrant numberCountry
Other governmentI-site ULNE - 3CLPRO-SCREEN-NMR France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: NMR Spectroscopy of the Main Protease of SARS-CoV-2 and Fragment-Based Screening Identify Three Protein Hotspots and an Antiviral Fragment.
Authors: Cantrelle, F.X. / Boll, E. / Brier, L. / Moschidi, D. / Belouzard, S. / Landry, V. / Leroux, F. / Dewitte, F. / Landrieu, I. / Dubuisson, J. / Deprez, B. / Charton, J. / Hanoulle, X.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
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: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3476
Polymers33,8581
Non-polymers4895
Water4,594255
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,69312
Polymers67,7152
Non-polymers97810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4330 Å2
ΔGint-27 kcal/mol
Surface area25180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.170, 53.560, 44.880
Angle α, β, γ (deg.)90.000, 101.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-694-

HOH

31A-698-

HOH

41A-721-

HOH

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33857.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (F01) corresponds to the fragment bound.
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-5P9 / N-(5-chloropyridin-2-yl)-3-oxo-2,3-dihydro-1H-indene-1-carboxamide / (1~{R})-~{N}-(5-chloranylpyridin-2-yl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide


Mass: 286.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M NaFORMATE, 20% PEG 3350, 10% GLYCEROL, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980111 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980111 Å / Relative weight: 1
ReflectionResolution: 1.47→48.442 Å / Num. obs: 45078 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 13.68
Reflection shellResolution: 1.47→1.56 Å / Num. unique obs: 7042 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.03phasing
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K3T

7k3t


Resolution: 1.474→48.442 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.805 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2157 2254 5 %
Rwork0.1814 42824 -
all0.183 --
obs-45078 99.396 %
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: 23.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.628 Å20 Å2-0.182 Å2
2--0.057 Å2-0 Å2
3----0.567 Å2
Refinement stepCycle: LAST / Resolution: 1.474→48.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 10 255 2647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132490
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172303
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.643388
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5755289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4645315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86523.008123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0415396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0241512
X-RAY DIFFRACTIONr_chiral_restr0.090.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.2280.2462
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22183
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21224
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2151
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.215
X-RAY DIFFRACTIONr_nbd_other0.1820.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.474-1.5120.3851550.3912959X-RAY DIFFRACTION93.0942
1.512-1.5530.3861630.3493080X-RAY DIFFRACTION100
1.553-1.5980.3321570.3182983X-RAY DIFFRACTION99.9682
1.598-1.6470.3391530.2922926X-RAY DIFFRACTION99.8703
1.647-1.7010.31490.2522831X-RAY DIFFRACTION99.9665
1.701-1.7610.2471440.2032725X-RAY DIFFRACTION99.9652
1.761-1.8270.2231390.1842651X-RAY DIFFRACTION100
1.827-1.9020.2241340.1852537X-RAY DIFFRACTION100
1.902-1.9860.1951300.1862470X-RAY DIFFRACTION99.9616
1.986-2.0830.2411210.1922306X-RAY DIFFRACTION100
2.083-2.1960.2451170.1962226X-RAY DIFFRACTION100
2.196-2.3290.2461130.1812129X-RAY DIFFRACTION99.9554
2.329-2.4890.2281030.1741972X-RAY DIFFRACTION100
2.489-2.6880.223980.1731847X-RAY DIFFRACTION99.9486
2.688-2.9440.208890.1671690X-RAY DIFFRACTION99.6081
2.944-3.2910.203810.1661544X-RAY DIFFRACTION99.9385
3.291-3.7980.157720.1431365X-RAY DIFFRACTION99.5842
3.798-4.6460.155600.1361154X-RAY DIFFRACTION99.6716
4.646-6.5480.171490.171916X-RAY DIFFRACTION100
6.548-48.4420.228270.172513X-RAY DIFFRACTION97.2973

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