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- PDB-8c9u: Crystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 8c9u
TitleCrystal structure of SARS-CoV-2 Mpro-Q189K mutant in complex with nirmatrelvir
ComponentsNon-structural protein 11
KeywordsANTIVIRAL PROTEIN / Mpro mutations main protease SARS-CoV-2
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 / endonuclease activity / 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 / methylation / 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 / host cell perinuclear region of cytoplasm / regulation of autophagy / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell nucleus / 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-4WI / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsEl Kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: Crystals / Year: 2025
Title: 13b-K and Nirmatrelvir Resistance Mutations of SARS-CoV-2 Main Protease: Structural, Biochemical, and Biophysical Characterization of Free Enzymes and Inhibitor Complexes
Authors: El Kilani, H. / Sun, X. / Ibrahim, M.F. / Curth, U. / Hilgenfeld, R.
History
DepositionJan 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 18, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.2Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Non-structural protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2002
Polymers33,6981
Non-polymers5021
Water4,143230
1
AAA: Non-structural protein 11
hetero molecules

AAA: Non-structural protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4004
Polymers67,3972
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3020 Å2
ΔGint-17 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.213, 64.476, 105.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-692-

HOH

21AAA-726-

HOH

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Components

#1: Protein Non-structural protein 11 / nsp11


Mass: 33698.469 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 (E. coli) / References: UniProt: P0DTC1
#2: Chemical ChemComp-4WI / (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / PF-07321332, bound form / nirmatrelvir, bound form / Paxlovid, bound form


Mass: 501.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium citrate tribasic dihydrate, 20% w/vPEG 3350

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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: Aug 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→41.58 Å / Num. obs: 31773 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.5
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1710 / CC1/2: 0.621

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→41.58 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.819 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2101 1544 4.864 %
Rwork0.1876 30201 -
all0.189 --
obs-31745 99.711 %
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: 21.676 Å2
Baniso -1Baniso -2Baniso -3
1--1.106 Å2-0 Å20 Å2
2--0.816 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 35 230 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132449
X-RAY DIFFRACTIONr_bond_other_d0.0030.0152275
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6433335
X-RAY DIFFRACTIONr_angle_other_deg1.4741.5775226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.67922.683123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24815388
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.586151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6831511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022809
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02577
X-RAY DIFFRACTIONr_nbd_refined0.2080.2454
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22160
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21182
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2180
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.320.213
X-RAY DIFFRACTIONr_nbd_other0.1990.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.217
X-RAY DIFFRACTIONr_mcbond_it1.9672.0851219
X-RAY DIFFRACTIONr_mcbond_other1.9432.0831218
X-RAY DIFFRACTIONr_mcangle_it2.8363.121522
X-RAY DIFFRACTIONr_mcangle_other2.8383.1221523
X-RAY DIFFRACTIONr_scbond_it2.962.3671229
X-RAY DIFFRACTIONr_scbond_other2.9592.3661230
X-RAY DIFFRACTIONr_scangle_it4.4483.4341810
X-RAY DIFFRACTIONr_scangle_other4.4473.4331811
X-RAY DIFFRACTIONr_lrange_it5.925.7322713
X-RAY DIFFRACTIONr_lrange_other5.85925.3542665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.2831210.2742189X-RAY DIFFRACTION99.8703
1.795-1.8450.2581130.2532132X-RAY DIFFRACTION99.911
1.845-1.8980.2471040.2322090X-RAY DIFFRACTION99.7273
1.898-1.9570.258900.222050X-RAY DIFFRACTION99.674
1.957-2.0210.253980.21969X-RAY DIFFRACTION99.9516
2.021-2.0920.2281060.1941883X-RAY DIFFRACTION99.8494
2.092-2.170.1911060.1891813X-RAY DIFFRACTION98.8157
2.17-2.2590.218790.1751797X-RAY DIFFRACTION99.8403
2.259-2.3590.215840.1721704X-RAY DIFFRACTION99.8325
2.359-2.4750.182920.1711633X-RAY DIFFRACTION99.7687
2.475-2.6080.223810.1811540X-RAY DIFFRACTION99.57
2.608-2.7660.213710.1791474X-RAY DIFFRACTION99.6774
2.766-2.9570.246760.1831401X-RAY DIFFRACTION99.8648
2.957-3.1940.176620.1831327X-RAY DIFFRACTION99.8562
3.194-3.4990.206700.1991191X-RAY DIFFRACTION99.8417
3.499-3.9110.227490.1891105X-RAY DIFFRACTION99.9134
3.911-4.5150.17570.153981X-RAY DIFFRACTION99.9038
4.515-5.5270.186390.157841X-RAY DIFFRACTION99.0991
5.527-7.8060.198320.203671X-RAY DIFFRACTION99.5751
7.806-41.550.173140.18410X-RAY DIFFRACTION98.8345

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