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- PDB-7mho: Ensemble refinement structure of apo/unliganded SARS-CoV-2 main p... -

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Basic information

Entry
Database: PDB / ID: 7mho
TitleEnsemble refinement structure of apo/unliganded SARS-CoV-2 main protease (Mpro) at 298 K
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / Coronavirus / main protease / 3CLpro / Mpro / apo / unliganded / ensemble refinement / temperature series / temperature / multitemperature
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / methyltransferase activity / DNA helicase / thiol-dependent deubiquitinase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein 2, SARS-CoV-like / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP1, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP7 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus RNA synthesis protein NSP10 / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP8 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus replicase NSP4, N-terminal / Peptidase C30, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein 6, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsEbrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
Department of Energy (DOE, United States)National Virtual Biotechnology Laboratory (NVBL) United States
Department of Energy (DOE, United States)Coronavirus CARES Act United States
Department of Energy (DOE, United States)BNL LDRD 20-042 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1605010 United States
CitationJournal: Biorxiv / Year: 2021
Title: The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9823
Polymers33,8261
Non-polymers1562
Water88349
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9646
Polymers67,6512
Non-polymers3134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3820 Å2
ΔGint-15 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)114.968, 54.622, 45.194
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number5
Space group name H-MC121
Number of models20
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

22A-538-

HOH

33A-504-

HOH

44A-518-

HOH

56A-510-

HOH

67A-539-

HOH

78A-507-

HOH

89A-523-

HOH

911A-529-

HOH

1012A-533-

HOH

1113A-519-

HOH

1214A-515-

HOH

1317A-532-

HOH

1417A-541-

HOH

1518A-504-

HOH

1618A-540-

HOH

1719A-508-

HOH

1819A-540-

HOH

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.05 Å3/Da / Density % sol: 40.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22% PEG 4000, 100 mM HEPES pH 7.0, 3--5% DMSO

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2020
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.88→56.295 Å / Num. obs: 22459 / % possible obs: 100 % / Redundancy: 6.7843 % / CC1/2: 0.9903 / Rmerge(I) obs: 0.1818 / Rpim(I) all: 0.0755 / Rrim(I) all: 0.1972 / Net I/σ(I): 5.0456 / Num. measured all: 152368
Reflection shell

Diffraction-ID: 1 / % possible obs: 100 %

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.88-1.91246.8592.35290.4035749010920.28510.96682.548
1.9124-1.94726.82671.8590.5432768011250.39480.76762.014
1.9472-1.98476.77331.45910.7755911160.53450.60461.5815
1.9847-2.02526.70871.3750.7637744011090.61090.5711.4909
2.0252-2.06926.58531.16350.925733611140.64730.48671.2632
2.0692-2.11746.15380.97471.0435684311120.67480.42541.0654
2.1174-2.17036.31670.86551.3224710011240.67040.37090.9429
2.1703-2.2296.79570.75661.5553761811210.75210.3130.8199
2.229-2.29466.73890.6321.9647758811260.79920.26210.6852
2.2946-2.36876.40230.54972.2282717711210.83620.23670.5995
2.3687-2.45336.9730.50692.5893776111130.88420.20610.5479
2.4533-2.55157.22860.45663.0479812511240.88170.1820.4921
2.5515-2.66777.25020.37413.8919793910950.92630.14860.4028
2.6677-2.80837.22810.31934.5187824011400.94390.1270.3439
2.8083-2.98437.14810.24866.0632796311140.96890.09990.2682
2.9843-3.21467.03840.19687.946806611460.97170.07960.2126
3.2146-3.53816.74730.151110.5113761111280.98350.06250.1637
3.5381-4.056.2930.11213.5192702311160.98770.04820.1221
4.05-5.1026.63790.094817.1623762711490.98780.04030.1032
5.102-56.32026.96930.092918.9633818211740.9870.03870.1009

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(phenix.ensemble_refinement:1.18.2_3874)refinement
xia20.6.464-g67f27e7a-dials-2.2data reduction
DIALS2.2.4-g04de204b4-releasedata scaling
PHASER1.18.2_3874phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YB7
Resolution: 1.88→49.14 Å / Cross valid method: THROUGHOUT
Details: The individual MODELs within this ensemble should not be interpreted individually. The ensemble as a whole is fitted to the data. Therefore, the structures represent a distribution that ...Details: The individual MODELs within this ensemble should not be interpreted individually. The ensemble as a whole is fitted to the data. Therefore, the structures represent a distribution that reflects fluctuations around ideal geometric values, i.e., each individual restraint in each individual structure does not necessarily have to fit the ideal geometric value and a degree of variation is expected.
RfactorNum. reflection% reflection
Rfree0.2077 1096 -
Rwork0.1667 --
obs0.1689 22270 99.16 %
Refinement stepCycle: final / Resolution: 1.88→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 0 2367
Num. residues----0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.88-1.970.41921210.31922489261094
1.97-2.070.32661460.273626142760100
2.07-2.20.26721380.241126632801100
2.2-2.370.27881270.213926752802100
2.37-2.610.26591460.189426322778100
2.61-2.980.24671250.179626832808100
2.98-3.760.19561510.151326862837100
3.76-49.140.14241420.12327322874100
Refinement TLS params.Method: fitted / Origin x: 12.24 Å / Origin y: 0.4674 Å / Origin z: 4.6073 Å
111213212223313233
T0.3896 Å20.0114 Å20.017 Å2-0.4611 Å2-0.0505 Å2--0.462 Å2
L0.999 °2-0.048 °20.1601 °2-1.421 °2-0.7195 °2--1.9087 °2
S-0.0024 Å °0.0018 Å °-0.0426 Å °-0.0299 Å °0.0133 Å °0.022 Å °0.0562 Å °-0.0347 Å °-0.0109 Å °
Refinement TLS groupSelection details: chain A

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