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- PDB-1uj1: Crystal structure of SARS Coronavirus Main Proteinase (3CLpro) -

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Basic information

Entry
Database: PDB / ID: 1uj1
TitleCrystal structure of SARS Coronavirus Main Proteinase (3CLpro)
Components3C-like proteinase
KeywordsHYDROLASE / anti-parallel b-barrel / anti-parallel a-helices
Function / homology
Function and homology information


positive regulation of ubiquitin-specific protease activity / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Lys48-specific deubiquitinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / 7-methylguanosine mRNA capping / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases ...positive regulation of ubiquitin-specific protease activity / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Lys48-specific deubiquitinase activity / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / 7-methylguanosine mRNA capping / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / 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 / suppression by virus of host type I interferon production / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / 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 / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / double-stranded RNA binding / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / : / endoplasmic reticulum membrane / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / 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 / Coronavirus replicase NSP15, N-terminal oligomerisation / RNA polymerase, N-terminal, coronavirus / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus proofreading exoribonuclease / Coronavirus 2'-O-methyltransferase / Coronavirus replicase NSP15, middle domain / 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 NSP3, N-terminal, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus Nsp3c-M domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / 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. / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP3, C-terminal / Non-structural protein 6, coronavirus / Coronavirus replicase NSP4, N-terminal / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus papain-like peptidase / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP4, C-terminal / RNA synthesis protein NSP10 superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus replicase NSP6 / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, H. / Yang, M. / Liu, Y. / Bartlam, M. / Ding, Y. / Lou, Z. / Sun, L. / Zhou, Z. / Ye, S. / Anand, K. ...Yang, H. / Yang, M. / Liu, Y. / Bartlam, M. / Ding, Y. / Lou, Z. / Sun, L. / Zhou, Z. / Ye, S. / Anand, K. / Pang, H. / Gao, G.F. / Hilgenfeld, R. / Rao, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor
Authors: Yang, H. / Yang, M. / Ding, Y. / Liu, Y. / Lou, Z. / Zhou, Z. / Sun, L. / Mo, L. / Ye, S. / Pang, H. / Gao, G.F. / Anand, K. / Bartlam, M. / Hilgenfeld, R. / Rao, Z.
History
DepositionJul 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,7532
Polymers67,7532
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-11 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)52.769, 97.150, 67.676
Angle α, β, γ (deg.)90.00, 103.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

#1: Protein 3C-like proteinase / Main Proteinase / 3CLPRO


Mass: 33876.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARSSevere acute respiratory syndrome / Plasmid: pGEX-6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3)
References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.43 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, MES, DMSO, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 %PEG60001reservoir
23 %DMSO1reservoir
31 mMdithiothreitol1reservoir
40.1 MMES1reservoirpH6.0
55 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9801 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51775 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.5
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 99.9 % / Redundancy: 3.7 % / Num. measured all: 190084 / Rmerge(I) obs: 0.107
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 4893 RANDOM
Rwork0.211 --
all0.235 52340 -
obs0.226 48577 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 0 300 4975
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.751
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.75

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