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- PDB-9epm: Mpro from SARS-CoV-2 with 4A mutation -

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Basic information

Entry
Database: PDB / ID: 9epm
TitleMpro from SARS-CoV-2 with 4A mutation
ComponentsNon-structural protein 11
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / oligomerization
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
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsPlewka, J. / Lis, K. / Czarna, A. / Pyrc, K. / Kantyka, T. / Chykunova, Y.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2017/27/B/NZ6/02488 Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: SARS-CoV-2 M pro oligomerization as a potential target for therapy.
Authors: Lis, K. / Plewka, J. / Menezes, F. / Bielecka, E. / Chykunova, Y. / Pustelny, K. / Niebling, S. / Garcia, A.S. / Garcia-Alai, M. / Popowicz, G.M. / Czarna, A. / Kantyka, T. / Pyrc, K.
History
DepositionMar 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)33,1201
Polymers33,1201
Non-polymers00
Water1,33374
1
A: Non-structural protein 11

A: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)66,2402
Polymers66,2402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2240 Å2
ΔGint-13 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.67, 53.32, 45.2
Angle α, β, γ (deg.)90, 101.97, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein 11 / nsp11


Mass: 33119.770 Da / Num. of mol.: 1 / Mutation: R4A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% Polyethylene glycol monomethyl ether 5.000, 200 mM Potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.98→48.125 Å / Num. obs: 18323 / % possible obs: 98.6 % / Redundancy: 6.3 % / CC1/2: 0.967 / Net I/σ(I): 8.87
Reflection shellResolution: 1.98→2.08 Å / Num. unique obs: 1210 / CC1/2: 0.346

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→48.125 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.374 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.218 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2663 917 5.005 %
Rwork0.1974 17405 -
all0.201 --
obs-18322 98.643 %
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: 52.564 Å2
Baniso -1Baniso -2Baniso -3
1-2.504 Å20 Å20.483 Å2
2---0.793 Å2-0 Å2
3----1.758 Å2
Refinement stepCycle: LAST / Resolution: 1.981→48.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 0 74 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122345
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162158
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.7983192
X-RAY DIFFRACTIONr_angle_other_deg0.7061.7294963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2475299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.68858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41310368
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.52210104
X-RAY DIFFRACTIONr_chiral_restr0.0830.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022784
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02546
X-RAY DIFFRACTIONr_nbd_refined0.1980.2442
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.22039
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21177
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21329
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2108
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1050.219
X-RAY DIFFRACTIONr_nbd_other0.1160.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.060.213
X-RAY DIFFRACTIONr_mcbond_it4.6365.051199
X-RAY DIFFRACTIONr_mcbond_other4.6365.051199
X-RAY DIFFRACTIONr_mcangle_it6.2269.0881497
X-RAY DIFFRACTIONr_mcangle_other6.2249.0891498
X-RAY DIFFRACTIONr_scbond_it5.4175.4661146
X-RAY DIFFRACTIONr_scbond_other5.4165.4671147
X-RAY DIFFRACTIONr_scangle_it7.6559.8691695
X-RAY DIFFRACTIONr_scangle_other7.6539.8691696
X-RAY DIFFRACTIONr_lrange_it9.46151.1872573
X-RAY DIFFRACTIONr_lrange_other9.46151.0482561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.981-2.0320.455680.43512790.43613510.8710.85999.70390.437
2.032-2.0870.401660.38912640.3913390.9020.88199.32790.39
2.087-2.1480.387640.3612050.36112780.890.8999.29580.363
2.148-2.2140.383620.34811780.3512580.8980.90898.56920.342
2.214-2.2860.389600.31111460.31512160.890.92599.17760.293
2.286-2.3660.368580.27410960.27811600.9180.94799.48280.256
2.366-2.4550.355570.24810880.25311520.9220.95799.39240.218
2.455-2.5550.332550.23610370.2410990.9240.96499.36310.208
2.555-2.6690.382520.2439940.2510510.9130.96299.52430.216
2.669-2.7990.382500.2419470.24810130.8940.96298.42050.207
2.799-2.9490.268470.228940.2229480.9640.96999.26160.189
2.949-3.1280.346450.1968630.2039210.9190.97698.58850.176
3.128-3.3420.244420.1697990.1738560.9580.98498.24770.154
3.342-3.6090.186390.1657380.1667900.9790.98598.35440.159
3.609-3.9510.226360.1746790.1777290.9660.98398.07960.171
3.951-4.4140.235330.1496270.1536780.9680.98797.34510.156
4.414-5.0890.193280.145340.1435850.9820.98996.06840.149
5.089-6.2160.244240.1774660.1815080.9840.98796.45670.188
6.216-8.7180.192200.1523650.1544070.9810.98794.59460.166
8.718-48.1250.163110.1332060.1342340.9840.98792.7350.169

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