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- PDB-9ewo: Mpro from SARS-CoV-2 with R4A R298A double mutations -

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Basic information

Entry
Database: PDB / ID: 9ewo
TitleMpro from SARS-CoV-2 with R4A R298A 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 / methylation / double membrane vesicle viral factory outer membrane ...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 / methylation / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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: 3.002 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1302
Polymers33,0341
Non-polymers961
Water362
1
A: Non-structural protein 11
hetero molecules

A: Non-structural protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2594
Polymers66,0672
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2570 Å2
ΔGint-49 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.326, 53.464, 46.081
Angle α, β, γ (deg.)90.000, 102.396, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Non-structural protein 11 / nsp11


Mass: 33033.652 Da / Num. of mol.: 1 / Mutation: R4A, R298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC1
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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, 0.12 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: 3→53.88 Å / Num. obs: 16784 / % possible obs: 91.5 % / Redundancy: 5.4 % / CC1/2: 0.992 / Net I/σ(I): 6.3
Reflection shellResolution: 3→3.22 Å / Num. unique obs: 1401 / CC1/2: 0.311

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.002→53.877 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.849 / SU B: 33.559 / SU ML: 0.567 / Cross valid method: FREE R-VALUE / ESU R Free: 0.709
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2754 198 4.833 %
Rwork0.1938 3899 -
all0.198 --
obs-4097 76.337 %
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: 74.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.315 Å20 Å20.586 Å2
2--0.149 Å2-0 Å2
3----0.657 Å2
Refinement stepCycle: LAST / Resolution: 3.002→53.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 5 2 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0112367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162189
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.6423220
X-RAY DIFFRACTIONr_angle_other_deg0.3941.5665031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8915299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.1559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46410376
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.95510106
X-RAY DIFFRACTIONr_chiral_restr0.0480.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_nbd_refined0.2320.2547
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.22202
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21196
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.272
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.221
X-RAY DIFFRACTIONr_nbd_other0.1780.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.23
X-RAY DIFFRACTIONr_mcbond_it4.8457.3131199
X-RAY DIFFRACTIONr_mcbond_other4.8457.3131199
X-RAY DIFFRACTIONr_mcangle_it7.85413.1181497
X-RAY DIFFRACTIONr_mcangle_other7.85113.1171498
X-RAY DIFFRACTIONr_scbond_it4.7427.7941168
X-RAY DIFFRACTIONr_scbond_other4.7137.7691165
X-RAY DIFFRACTIONr_scangle_it7.99714.1821723
X-RAY DIFFRACTIONr_scangle_other7.95314.1371718
X-RAY DIFFRACTIONr_lrange_it12.48174.5392678
X-RAY DIFFRACTIONr_lrange_other12.47974.5372679
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
3.002-3.080.31640.288520.2914110.9670.95113.62530.289
3.08-3.1640.21230.343720.3383660.9920.92520.49180.34
3.164-3.2550.26640.3631270.3613710.7770.91735.310.356
3.255-3.3550.28880.3091670.3083680.9680.93547.55430.315
3.355-3.4650.22120.2812100.2783420.9550.94564.91230.266
3.465-3.5860.397120.2562670.2623400.9010.95382.05880.244
3.586-3.720.275150.2452950.2473190.9450.95997.17870.215
3.72-3.8720.258150.243100.2413250.980.9641000.218
3.872-4.0430.24150.212820.2112970.9640.9741000.19
4.043-4.2390.266140.1832780.1872920.9790.981000.176
4.239-4.4670.311100.1642650.172750.9480.9821000.158
4.467-4.7360.275130.152430.1562560.9480.9851000.147
4.736-5.060.271160.1682390.1742550.9550.9821000.167
5.06-5.4610.27390.1992200.2022290.9170.9791000.196
5.461-5.9760.542150.2312010.252160.9070.9751000.226
5.976-6.6710.151110.2091870.2061980.9790.9761000.214
6.671-7.6840.19390.1421650.1451740.9810.9861000.157
7.684-9.3630.44350.1151370.1221420.9270.9911000.128
9.363-13.0460.06840.1261110.1241150.9930.9911000.153
13.046-53.8770.38240.181710.186760.8330.97198.68420.226

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