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- PDB-9eur: Mpro WT from SARS-CoV-2 with 298Q mutation -

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Basic information

Entry
Database: PDB / ID: 9eur
TitleMpro WT from SARS-CoV-2 with 298Q mutation
ComponentsReplicase polyprotein 1a
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / oligomerization
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / 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 / Betacoronavirus Nsp3c-M domain profile. ...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 / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / 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 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: 2.113 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 28, 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: Replicase polyprotein 1a


Theoretical massNumber of molelcules
Total (without water)33,2061
Polymers33,2061
Non-polymers00
Water46826
1
A: Replicase polyprotein 1a

A: Replicase polyprotein 1a


Theoretical massNumber of molelcules
Total (without water)66,4122
Polymers66,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2490 Å2
ΔGint-13 kcal/mol
Surface area25820 Å2
Unit cell
Length a, b, c (Å)44.979, 53.68, 113.957
Angle α, β, γ (deg.)90, 100.819, 90
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-423-

HOH

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Components

#1: Protein Replicase polyprotein 1a / ORF1a polyprotein


Mass: 33205.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B1JMI3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.03 Å3/Da / Density % sol: 39.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.11→48.402 Å / Num. obs: 15279 / % possible obs: 99.1 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.086 / Rrim(I) all: 0.162 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.96-48.4026.10.0712160.9950.0430.084
2.11-2.1772.15312460.4391.3282.538

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.113→48.402 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.601 / SU ML: 0.312 / Cross valid method: FREE R-VALUE / ESU R: 0.308 / ESU R Free: 0.244
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2806 774 5.066 %
Rwork0.2102 14503 -
all0.214 --
obs-15277 98.893 %
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: 62.476 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å2-0 Å21.387 Å2
2---2.225 Å2-0 Å2
3---4.813 Å2
Refinement stepCycle: LAST / Resolution: 2.113→48.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 0 26 2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122375
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162205
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.8043228
X-RAY DIFFRACTIONr_angle_other_deg0.6851.7365065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2985299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.568511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31510382
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.72610108
X-RAY DIFFRACTIONr_chiral_restr0.0830.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022825
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02565
X-RAY DIFFRACTIONr_nbd_refined0.1860.2404
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1520.21938
X-RAY DIFFRACTIONr_nbtor_refined0.1610.21164
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.21298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.230
X-RAY DIFFRACTIONr_nbd_other0.1130.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.29
X-RAY DIFFRACTIONr_mcbond_it5.2385.9411199
X-RAY DIFFRACTIONr_mcbond_other5.2265.9411199
X-RAY DIFFRACTIONr_mcangle_it7.33910.7111497
X-RAY DIFFRACTIONr_mcangle_other7.33710.7121498
X-RAY DIFFRACTIONr_scbond_it5.9936.5341176
X-RAY DIFFRACTIONr_scbond_other5.996.5351177
X-RAY DIFFRACTIONr_scangle_it8.95711.7681731
X-RAY DIFFRACTIONr_scangle_other8.95511.7681732
X-RAY DIFFRACTIONr_lrange_it14.19461.6182513
X-RAY DIFFRACTIONr_lrange_other14.19261.622514
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
2.113-2.1670.345500.42110690.41711200.7580.76799.91070.413
2.167-2.2270.413510.36810350.3710900.7880.84899.6330.357
2.227-2.2910.423540.35510260.35810850.870.88199.53920.339
2.291-2.3610.364630.3329760.33410440.8920.90499.52110.315
2.361-2.4390.357530.3129490.31410090.9270.9299.30620.296
2.439-2.5240.375560.2839340.2879980.8940.94199.19840.264
2.524-2.6190.323450.2738830.2759410.9280.94598.61850.256
2.619-2.7260.555260.248460.2489000.8680.9696.88890.224
2.726-2.8460.375510.2368270.2438830.9230.96399.43370.219
2.846-2.9850.368360.2117990.2178390.9130.96999.52320.198
2.985-3.1460.386300.227580.2267930.9080.96799.36950.212
3.146-3.3360.236320.2097170.217610.960.97198.42310.206
3.336-3.5650.259330.2176520.226990.9620.96797.99710.214
3.565-3.8490.289350.2056130.2096690.9470.9796.8610.21
3.849-4.2130.252410.1855560.196100.9630.97997.86890.2
4.213-4.7060.236390.1465230.1535620.9570.9861000.164
4.706-5.4260.214350.1654590.1694980.9780.98699.19680.192
5.426-6.6240.214140.1673890.1694140.9690.98897.3430.188
6.624-9.2810.154170.1443050.1453320.9870.98896.9880.169
9.281-48.4020.368130.1581870.1682000.9290.9861000.185

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