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- PDB-9ewm: Mpro from SARS-CoV-2 with R4Q R298Q double mutations -

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Basic information

Entry
Database: PDB / ID: 9ewm
TitleMpro from SARS-CoV-2 with R4Q R298Q double mutations
ComponentsNon-structural protein 11
KeywordsANTIVIRAL PROTEIN / sars-cov-2 / protease / 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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsPlewka, J. / Lis, K. / Chykunova, Y. / Czarna, A. / Kantyka, T. / Pyrc, K.
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
DepositionApr 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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)33,1481
Polymers33,1481
Non-polymers00
Water00
1
A: Non-structural protein 11

A: Non-structural protein 11


Theoretical massNumber of molelcules
Total (without water)66,2962
Polymers66,2962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area25780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.136, 53.802, 45.286
Angle α, β, γ (deg.)90.000, 100.174, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein 11 / nsp11


Mass: 33147.754 Da / Num. of mol.: 1 / Mutation: R4Q, R298Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC1

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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: 38.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.63→57.65 Å / Num. obs: 12088 / % possible obs: 83.1 % / Redundancy: 6.5 % / CC1/2: 0.989 / Net I/σ(I): 6.3
Reflection shellResolution: 2.63→2.85 Å / Num. unique obs: 979 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→48.802 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / Cross valid method: FREE R-VALUE / ESU R Free: 0.552
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.336 346 4.823 %
Rwork0.2392 6828 -
all0.244 --
obs-7174 85.476 %
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: 44.221 Å2
Baniso -1Baniso -2Baniso -3
1--0.527 Å20 Å2-0.398 Å2
2---0.611 Å2-0 Å2
3---1.203 Å2
Refinement stepCycle: LAST / Resolution: 2.63→48.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 0 0 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122372
X-RAY DIFFRACTIONr_angle_refined_deg1.61.83226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8035299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.41359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99910380
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.14310108
X-RAY DIFFRACTIONr_chiral_restr0.0710.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021826
X-RAY DIFFRACTIONr_nbd_refined0.250.21072
X-RAY DIFFRACTIONr_nbtor_refined0.320.21638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.288
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0740.26
X-RAY DIFFRACTIONr_mcbond_it10.6454.0681199
X-RAY DIFFRACTIONr_mcangle_it14.4417.2731497
X-RAY DIFFRACTIONr_scbond_it13.2064.5991173
X-RAY DIFFRACTIONr_scangle_it17.2388.1481729
X-RAY DIFFRACTIONr_lrange_it19.30349.3143534
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
2.63-2.6980.70610.3461080.3516441.4140.89216.92550.35
2.698-2.7720.64990.3472060.3585790.640.91437.1330.347
2.772-2.8520.455190.3793920.3825740.8010.89271.60280.384
2.852-2.940.382270.3544730.3565690.9150.91187.87350.35
2.94-3.0360.425320.3014370.315400.8680.93686.85190.291
3.036-3.1420.435260.3364850.345250.9070.92297.33330.319
3.142-3.260.482230.3034950.3115180.8670.9361000.292
3.26-3.3920.347180.2734790.2754970.930.9491000.255
3.392-3.5420.42230.2844590.2894820.8720.9451000.267
3.542-3.7140.374260.2674140.2744400.9160.9531000.257
3.714-3.9140.379270.2424040.254310.8940.9611000.234
3.914-4.150.315200.2273890.2314090.9420.9661000.224
4.15-4.4340.21170.2123730.2123900.9650.971000.22
4.434-4.7860.346170.1873380.1943550.9450.981000.194
4.786-5.2380.185100.23250.23350.9780.9731000.216
5.238-5.8470.386110.2383000.2433110.8930.9671000.255
5.847-6.7360.202150.212490.212640.9680.9741000.228
6.736-8.2110.222120.1762150.1792270.9760.9821000.218
8.211-11.4510.275100.1421790.1491890.9690.9881000.184
11.451-48.8020.47830.1891080.1941120.6450.9899.10710.233

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