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Basic information

Entry
Database: PDB / ID: 3sna
TitleCrystal structure of SARS coronavirus main protease complexed with Ac-NSFSQ-H (soaking)
Components
  • 3C-like proteinase
  • Peptide aldehyde inhibitor Ac-NSFSQ-H
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 3C-like proteinase / protease / Ac-NSFSQ-H / ACTIVE SITE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of ubiquitin-specific protease activity / Maturation of replicase proteins / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / 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 / Maturation of replicase proteins / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / 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 / 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 / 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 / Nonstructural protein 14, 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. ...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 / Nonstructural protein 14, 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. / 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. / 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 / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP1 superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein 2, SARS-CoV-like / 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 NSP1, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein 6, coronavirus / Peptidase C30, domain 3, 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
Similarity search - Domain/homology
Peptide aldehyde inhibitor Ac-NSFSQ-H / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsZhu, L. / Hilgenfeld, R.
CitationJournal: Antiviral Res. / Year: 2011
Title: Peptide aldehyde inhibitors challenge the substrate specificity of the SARS-coronavirus main protease.
Authors: Zhu, L. / George, S. / Schmidt, M.F. / Al-Gharabli, S.I. / Rademann, J. / Hilgenfeld, R.
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Structure summary
Revision 1.2Nov 9, 2011Group: Database references
Revision 1.3Dec 12, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
H: Peptide aldehyde inhibitor Ac-NSFSQ-H


Theoretical massNumber of molelcules
Total (without water)33,9382
Polymers33,9382
Non-polymers00
Water25214
1
A: 3C-like proteinase
H: Peptide aldehyde inhibitor Ac-NSFSQ-H

A: 3C-like proteinase
H: Peptide aldehyde inhibitor Ac-NSFSQ-H


Theoretical massNumber of molelcules
Total (without water)67,8754
Polymers67,8754
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4720 Å2
ΔGint-19 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)107.870, 82.090, 53.080
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / nsp5


Mass: 33344.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Production host: Escherichia coli (E. coli)
References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide Peptide aldehyde inhibitor Ac-NSFSQ-H


Type: PolypeptidePeptide / Class: Enzyme inhibitor / Mass: 593.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: Peptide aldehyde inhibitor Ac-NSFSQ-H
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 8% PEG 6000, 0.1 M MES, 3% MPD, 3% DMSO, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 3.05→64.56 Å / Num. all: 8643 / Num. obs: 8643 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 89.3 Å2
Reflection shellResolution: 3.05→3.129 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→42.25 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.912 / SU B: 45.407 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 410 4.7 %RANDOM
Rwork0.19004 ---
obs0.19314 8233 99.92 %-
all-8643 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.08 Å2
2--0.11 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.05→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 14 2390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222432
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9523297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5755303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.48824.312109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.86915391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6171512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211846
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6421.51524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21722455
X-RAY DIFFRACTIONr_scbond_it1.4483908
X-RAY DIFFRACTIONr_scangle_it2.4774.5842
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 35 -
Rwork0.296 615 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2744-0.5529-0.1471.3341-0.65011.357-0.00080.1369-0.09230.0241-0.0431-0.0272-0.00720.01920.04390.08170.066-0.01080.07990.0030.061.34930.792215.0836
221.6804-3.2225-2.5380.47970.37730.3381-0.3681-1.2989-0.46010.07310.24080.0636-0.11030.30430.12730.8468-0.4265-0.20210.76480.19540.272518.2823.829922.7305
31.2359-1.18590.30881.63950.12710.46750.23860.1715-0.1428-0.1751-0.19680.12750.0425-0.0203-0.04180.24030.0091-0.06870.14530.02320.0377-2.62454.949312.7556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2H0 - 5
3X-RAY DIFFRACTION3A302 - 315

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