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- PDB-7z0p: SARS-COV2 Main Protease in complex with inhibitor MG-131 -

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Basic information

Entry
Database: PDB / ID: 7z0p
TitleSARS-COV2 Main Protease in complex with inhibitor MG-131
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / Inhibitor complex / SARS-COV2 / SARS-COV2 Mpro
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 / endonuclease activity / 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 / methylation / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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 / viral protein processing / host cell perinuclear region of cytoplasm / 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 / Betacoronavirus single-stranded poly(A) binding domain ...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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus replicase NSP1 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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-I8H / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsEl Kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Molecules / Year: 2022
Title: From Repurposing to Redesign: Optimization of Boceprevir to Highly Potent Inhibitors of the SARS-CoV-2 Main Protease.
Authors: Gohl, M. / Zhang, L. / El Kilani, H. / Sun, X. / Zhang, K. / Bronstrup, M. / Hilgenfeld, R.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Sep 18, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
AAA: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1383
Polymers33,5501
Non-polymers5882
Water66737
1
AAA: 3C-like proteinase nsp5
hetero molecules

AAA: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2766
Polymers67,1002
Non-polymers1,1754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3160 Å2
ΔGint-16 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.716, 51.667, 45.451
Angle α, β, γ (deg.)90.000, 103.335, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33550.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-I8H / (1~{R},2~{S},5~{S})-3-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-~{N}-[(2~{S},3~{R})-4-(methylamino)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide


Mass: 564.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48N6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.94 Å3/Da / Density % sol: 36.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M MMT, pH 9.0 plus 25% w/v polyethylenglycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.52→46.81 Å / Num. obs: 49867 / % possible obs: 99 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.2
Reflection shellResolution: 2.52→2.62 Å / Num. unique obs: 7839 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y2e

6y2e


Resolution: 2.52→46.81 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.865 / SU B: 19.761 / SU ML: 0.392 / Cross valid method: FREE R-VALUE / ESU R Free: 0.402
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2898 420 4.799 %
Rwork0.2035 8332 -
all0.208 --
obs-8752 98.781 %
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: 44.003 Å2
Baniso -1Baniso -2Baniso -3
1-1.881 Å2-0 Å2-1.283 Å2
2--0.932 Å2-0 Å2
3----1.982 Å2
Refinement stepCycle: LAST / Resolution: 2.52→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 41 37 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152275
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6453327
X-RAY DIFFRACTIONr_angle_other_deg1.1851.5765222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3245303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07622.56125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08415385
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg7.442151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4261511
X-RAY DIFFRACTIONr_chiral_restr0.2520.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
X-RAY DIFFRACTIONr_nbd_refined0.2250.2628
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22434
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.150.229
X-RAY DIFFRACTIONr_nbd_other0.2210.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2560.210
X-RAY DIFFRACTIONr_mcbond_it3.154.5531215
X-RAY DIFFRACTIONr_mcbond_other3.1514.5511214
X-RAY DIFFRACTIONr_mcangle_it4.9816.8241517
X-RAY DIFFRACTIONr_mcangle_other4.9796.8281518
X-RAY DIFFRACTIONr_scbond_it3.1714.8291227
X-RAY DIFFRACTIONr_scbond_other3.174.8281228
X-RAY DIFFRACTIONr_scangle_it5.1837.1151807
X-RAY DIFFRACTIONr_scangle_other5.1827.1141808
X-RAY DIFFRACTIONr_lrange_it7.92254.3932781
X-RAY DIFFRACTIONr_lrange_other7.92154.3972781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.620.318270.326597X-RAY DIFFRACTION97.0451
2.581-2.6520.361350.329594X-RAY DIFFRACTION99.5253
2.652-2.7280.43210.313600X-RAY DIFFRACTION99.8392
2.728-2.8120.38320.303560X-RAY DIFFRACTION99.6633
2.812-2.9040.321240.281544X-RAY DIFFRACTION99.6491
2.904-3.0060.364330.263541X-RAY DIFFRACTION99.1364
3.006-3.1190.279210.242510X-RAY DIFFRACTION99.812
3.119-3.2460.288340.234488X-RAY DIFFRACTION99.4286
3.246-3.390.276200.202466X-RAY DIFFRACTION99.1837
3.39-3.5540.299190.176453X-RAY DIFFRACTION98.9518
3.554-3.7460.258190.143433X-RAY DIFFRACTION97.6242
3.746-3.9720.141220.128389X-RAY DIFFRACTION96.2529
3.972-4.2450.284200.127366X-RAY DIFFRACTION93.9173
4.245-4.5820.195170.124367X-RAY DIFFRACTION98.4615
4.582-5.0160.32680.121338X-RAY DIFFRACTION99.7118
5.016-5.6030.23240.153298X-RAY DIFFRACTION100
5.603-6.4580.256130.198272X-RAY DIFFRACTION100
6.458-7.8830.298110.187226X-RAY DIFFRACTION100
7.883-11.0370.383110.233184X-RAY DIFFRACTION100

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