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- PDB-7c2y: The crystal structure of COVID-2019 main protease in the apo state -

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Entry
Database: PDB / ID: 7c2y
TitleThe crystal structure of COVID-2019 main protease in the apo state
Components3C-like proteinase
KeywordsVIRAL PROTEIN / COVID-2019 / protease
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 / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / 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 / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / 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 / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / suppression by virus of host toll-like receptor signaling pathway / protein K48-linked deubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / transcription, RNA-templated / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / cysteine-type peptidase activity / suppression by virus of host TRAF activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / helicase activity / ubiquitinyl hydrolase 1 / Transferases; Transferring one-carbon groups; Methyltransferases / viral transcription / 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 / endonuclease activity / RNA-directed RNA polymerase / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / Hydrolases; Acting on ester bonds / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus replicase NSP3, N-terminal / Betacoronavirus SUD-C domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / RNA polymerase, N-terminal, coronaviral / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Betacoronavirus Nsp3c-M domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein NSP1, betacoronavirus / 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 / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein 6, betacoronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Betacoronavirus nucleic acid-binding (NAR) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP3A domain-like superfamily / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / 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. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Lipocalin signature. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus papain-like peptidase / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP4, C-terminal, 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 / RNA synthesis protein NSP10, coronavirus / Peptidase C30, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsZhou, X.L. / Zhong, F.L. / Lin, C. / Zhou, H. / Hu, X.H. / Wang, Q.S. / Li, J. / Zhang, J.
CitationJournal: To Be Published
Title: COVID-2019 main protease in the apo state
Authors: Zhou, X.L. / Zhong, F.L. / Lin, C. / Zhou, H. / Hu, X.H. / Wang, Q.S. / Li, J. / Zhang, J.
History
DepositionMay 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)65,9492
Polymers65,9492
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-8 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)67.880, 102.340, 103.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 3C-like proteinase / pp1ab / ORF1ab polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / ...pp1ab / ORF1ab polyprotein / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 32974.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 10% Propanol ,20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.91→72.77 Å / Num. obs: 743898 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.9734754348 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.9
Reflection shellResolution: 1.91→1.96 Å / Rmerge(I) obs: 1.407 / Num. unique obs: 54845

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LU7
Resolution: 1.91→72.77 Å / SU ML: 0.225796705835 / Cross valid method: NONE / σ(F): 1.34859193948 / Phase error: 25.6189332474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261688497256 3816 3.53732920521 %
Rwork0.220077061897 104062 -
obs0.221504456976 107878 99.8454347725 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.4808669861 Å2
Refinement stepCycle: LAST / Resolution: 1.91→72.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 0 185 4383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008096994316384287
X-RAY DIFFRACTIONf_angle_d0.8870356101385844
X-RAY DIFFRACTIONf_chiral_restr0.0542323037488677
X-RAY DIFFRACTIONf_plane_restr0.00603843014791760
X-RAY DIFFRACTIONf_dihedral_angle_d16.82230291791448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93421430.2851183787083862X-RAY DIFFRACTION99.7012696042
1.9342-1.95960.3577838648071300.2806909680223838X-RAY DIFFRACTION99.5983935743
1.9596-1.98650.3147502995181460.2809600257153863X-RAY DIFFRACTION99.9750623441
1.9865-2.01490.3034070015521390.2784984289193852X-RAY DIFFRACTION99.924887331
2.0149-2.04490.3232292886431420.2658875800213844X-RAY DIFFRACTION99.9247931812
2.0449-2.07690.2917548648351450.2573492726413882X-RAY DIFFRACTION99.8512273742
2.0769-2.1110.2636696802351460.2467974247723841X-RAY DIFFRACTION99.9749247743
2.111-2.14740.2594862679681360.2415266047343832X-RAY DIFFRACTION99.849018621
2.1474-2.18640.2670238522971440.24051513383863X-RAY DIFFRACTION99.6518279035
2.1864-2.22850.2684278792441510.2407793807543847X-RAY DIFFRACTION99.9250187453
2.2285-2.27390.2888450036921280.2407350531473878X-RAY DIFFRACTION99.8006975585
2.2739-2.32340.25928103051400.2321624280583852X-RAY DIFFRACTION99.9249061327
2.3234-2.37740.3127155613071490.2347729752533820X-RAY DIFFRACTION99.823943662
2.3774-2.43690.243209626121390.226784726923880X-RAY DIFFRACTION99.9254102437
2.4369-2.50280.2898917430061430.2327521362733866X-RAY DIFFRACTION100
2.5028-2.57640.2933709809041380.2466603988053834X-RAY DIFFRACTION99.8491704374
2.5764-2.65960.3632840789341400.2360625213343879X-RAY DIFFRACTION99.9751243781
2.6596-2.75470.3028799010471420.2278515539033845X-RAY DIFFRACTION99.9248120301
2.7547-2.8650.2517846569321330.2273541900113877X-RAY DIFFRACTION99.9501495513
2.865-2.99540.2318408880521460.2229743909543842X-RAY DIFFRACTION99.9749310604
2.9954-3.15330.2841301156921400.2209402922123880X-RAY DIFFRACTION99.9502734958
3.1533-3.35080.2606331115271390.2288029658633857X-RAY DIFFRACTION99.9
3.3508-3.60960.2667515968811470.2168794948523831X-RAY DIFFRACTION99.9748680573
3.6096-3.97280.2481489538591450.2003340189133882X-RAY DIFFRACTION100
3.9728-4.54760.1809953684241390.1689551455413859X-RAY DIFFRACTION100
4.5476-5.72910.2836765689661450.1911030347123846X-RAY DIFFRACTION99.9749498998
5.7291-72.770.218765787481410.2078392001563810X-RAY DIFFRACTION98.7503124219

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