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- PDB-7bal: Crystal structure of SARS-CoV-2 main protease treated with ebsele... -

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Entry
Database: PDB / ID: 7bal
TitleCrystal structure of SARS-CoV-2 main protease treated with ebselen derivative of MR6-31-2
ComponentsMain Protease
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / COVID19 / ebselen
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / 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 ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / 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 / suppression by virus of host toll-like receptor signaling pathway / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / 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 / DNA helicase / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / endonuclease activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / viral RNA genome replication / RNA helicase activity / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / 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. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) 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 / Non-structural protein NSP15, middle domain superfamily / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / RNA polymerase, N-terminal, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP1 superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain 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 Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP1, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / 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 RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a 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 / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Papain-like viral protease, palm and finger domains, coronavirus / Peptidase family C16 domain profile. / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Coronavirus endopeptidase C30 / Non-structural protein NSP8, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP6 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP8 superfamily, coronavirus / Peptidase C30, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal
Similarity search - Domain/homology
SELENIUM ATOM / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsAmporndanai, K. / O'Neill, P.M. / Hasnain, S.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: Inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives.
Authors: Amporndanai, K. / Meng, X. / Shang, W. / Jin, Z. / Rogers, M. / Zhao, Y. / Rao, Z. / Liu, Z.J. / Yang, H. / Zhang, L. / O'Neill, P.M. / Samar Hasnain, S.
History
DepositionDec 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Main Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9052
Polymers33,8261
Non-polymers791
Water2,504139
1
A: Main Protease
hetero molecules

A: Main Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8094
Polymers67,6512
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2800 Å2
ΔGint-22 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)114.004, 53.622, 44.545
Angle α, β, γ (deg.)90.000, 100.892, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

21A-593-

HOH

31A-596-

HOH

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Components

#1: Protein Main Protease / pp1ab / ORF1ab polyprotein


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: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SE / SELENIUM ATOM / Selenium


Mass: 78.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Se / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 200mM ammonium chloride, 5%glycerol and 20% polyethylene glycol mw. 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 10, 2020 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→33.867 Å / Num. obs: 22635 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.069 / Rrim(I) all: 0.102 / Χ2: 0.82 / Net I/σ(I): 8.6
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.079 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1364 / CC1/2: 0.446 / Rpim(I) all: 0.971 / Rrim(I) all: 1.456 / Χ2: 0.69 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y2e
Resolution: 1.85→33.867 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.076 / SU ML: 0.165 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.159
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.249 1159 5.123 %
Rwork0.2239 21465 -
all0.225 --
obs-22624 99.81 %
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: 36.114 Å2
Baniso -1Baniso -2Baniso -3
1-2.401 Å20 Å20.48 Å2
2---0.621 Å20 Å2
3----1.829 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 1 139 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122392
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.633256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7695307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35823.504117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11515381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9831510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021848
X-RAY DIFFRACTIONr_nbd_refined0.2190.21079
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2134
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4260.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2490.211
X-RAY DIFFRACTIONr_mcbond_it3.2883.431219
X-RAY DIFFRACTIONr_mcangle_it4.3145.1311529
X-RAY DIFFRACTIONr_scbond_it4.0843.7361173
X-RAY DIFFRACTIONr_scangle_it5.7215.4691727
X-RAY DIFFRACTIONr_lrange_it7.58465.33810275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.384950.3681544X-RAY DIFFRACTION99.8173
1.898-1.950.365680.3161528X-RAY DIFFRACTION99.6255
1.95-2.0060.421860.3281516X-RAY DIFFRACTION99.8131
2.006-2.0680.301680.3181459X-RAY DIFFRACTION99.9346
2.068-2.1360.33790.2941403X-RAY DIFFRACTION99.6637
2.136-2.2110.305850.2771347X-RAY DIFFRACTION99.7215
2.211-2.2940.286670.2811320X-RAY DIFFRACTION99.7842
2.294-2.3880.307680.2691261X-RAY DIFFRACTION99.9248
2.388-2.4930.286540.2551243X-RAY DIFFRACTION99.6925
2.493-2.6150.333670.281174X-RAY DIFFRACTION100
2.615-2.7560.382650.2561093X-RAY DIFFRACTION99.9137
2.756-2.9230.224660.2371032X-RAY DIFFRACTION100
2.923-3.1240.238420.2141008X-RAY DIFFRACTION100
3.124-3.3730.257440.202928X-RAY DIFFRACTION100
3.373-3.6940.206480.196862X-RAY DIFFRACTION100
3.694-4.1280.205390.173769X-RAY DIFFRACTION99.7531
4.128-4.7620.184500.151665X-RAY DIFFRACTION99.4437
4.762-5.8220.145290.172592X-RAY DIFFRACTION100
5.822-8.1890.238220.191458X-RAY DIFFRACTION100
8.189-33.8670.144170.144263X-RAY DIFFRACTION97.9021

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