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- PDB-8cac: Crystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 8cac
TitleCrystal structure of SARS-CoV-2 Mpro-H172Y mutant in complex with 13b-K
Components3C-like proteinase nsp5
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-O6K / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsIbrahim, M. / El 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 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Sep 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: 3C-like proteinase nsp5
BBB: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9775
Polymers66,7502
Non-polymers1,2273
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-25 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.032, 101.709, 103.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 33375.043 Da / Num. of mol.: 2
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, SARS coronavirus main proteinase
#2: Chemical ChemComp-O6K / ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate / (S,S,S)-13b / 13b-K / ketoamide inhibitor 13b (bound)


Mass: 595.687 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Bis-Tris, Potassium citrate tribasic monohydrate, PEG 3350, Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 2.13→46.061 Å / Num. obs: 40658 / % possible obs: 99.81 % / Redundancy: 7.5 % / Biso Wilson estimate: 42.05 Å2 / CC1/2: 0.998 / CC star: 1 / Net I/σ(I): 9.71
Reflection shellResolution: 2.15→2.23 Å / Mean I/σ(I) obs: 0.94 / Num. unique obs: 3883 / CC1/2: 0.587 / CC star: 0.86 / % possible all: 99.79

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Processing

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

6y2e


Resolution: 2.13→46.061 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.185 / SU B: 11.479 / SU ML: 0.255 / Average fsc free: 0.7286 / Average fsc work: 0.7357 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.21
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2719 2045 5.03 %
Rwork0.2117 38613 -
all0.215 --
obs-40658 99.782 %
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: 52.502 Å2
Baniso -1Baniso -2Baniso -3
1--3.983 Å2-0 Å20 Å2
2--5.592 Å2-0 Å2
3----1.609 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 87 122 4875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134874
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154515
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6426628
X-RAY DIFFRACTIONr_angle_other_deg1.2371.57510370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9625603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56722.857245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32115767
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg4.279152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.251522
X-RAY DIFFRACTIONr_chiral_restr0.0640.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021167
X-RAY DIFFRACTIONr_nbd_refined0.2030.2874
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.24273
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22342
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.212
X-RAY DIFFRACTIONr_nbd_other0.2290.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_mcbond_it3.9735.4052412
X-RAY DIFFRACTIONr_mcbond_other3.9625.4022410
X-RAY DIFFRACTIONr_mcangle_it6.1548.0853012
X-RAY DIFFRACTIONr_mcangle_other6.1458.0863012
X-RAY DIFFRACTIONr_scbond_it4.225.7762462
X-RAY DIFFRACTIONr_scbond_other4.2195.7762463
X-RAY DIFFRACTIONr_scangle_it6.6338.4833609
X-RAY DIFFRACTIONr_scangle_other6.6328.4833610
X-RAY DIFFRACTIONr_lrange_it9.57162.455165
X-RAY DIFFRACTIONr_lrange_other9.57662.4125151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.1860.4041330.4072799X-RAY DIFFRACTION99.3225
2.186-2.2450.3981180.3782754X-RAY DIFFRACTION99.8262
2.245-2.310.4161390.3692696X-RAY DIFFRACTION99.7888
2.31-2.3810.3731320.3272592X-RAY DIFFRACTION99.8534
2.381-2.4590.4041380.3212523X-RAY DIFFRACTION99.7376
2.459-2.5460.3841300.2882433X-RAY DIFFRACTION99.8831
2.546-2.6420.3181370.2672336X-RAY DIFFRACTION99.758
2.642-2.7490.291160.242286X-RAY DIFFRACTION99.8753
2.749-2.8710.3161290.2142164X-RAY DIFFRACTION99.9128
2.871-3.0110.2851290.2092081X-RAY DIFFRACTION99.9096
3.011-3.1740.2751090.1961979X-RAY DIFFRACTION99.9521
3.174-3.3660.2441000.191891X-RAY DIFFRACTION99.9498
3.366-3.5980.252940.1841796X-RAY DIFFRACTION99.7888
3.598-3.8850.243990.191647X-RAY DIFFRACTION99.6575
3.885-4.2550.241910.1681549X-RAY DIFFRACTION99.8782
4.255-4.7550.198600.151406X-RAY DIFFRACTION99.9318
4.755-5.4870.248650.1631245X-RAY DIFFRACTION99.8476
5.487-6.710.229670.2011068X-RAY DIFFRACTION100
6.71-9.4490.165410.154855X-RAY DIFFRACTION99.4451
9.449-46.0610.304180.198513X-RAY DIFFRACTION98.3333

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