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- PDB-3m3s: Crystal structure of SARS-COV main protease Asn214Ala mutant with... -

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Basic information

Entry
Database: PDB / ID: 3m3s
TitleCrystal structure of SARS-COV main protease Asn214Ala mutant with authorize N-terminus
Components3C-like proteinase
KeywordsHYDROLASE / SARS coronavirus protease N214A mutation
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 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShi, J.H. / Song, J.X.
CitationJournal: To be Published
Title: Dynamical Inactivation of the Catalytic Machinery of the SARS-CoV 3C-Like Protease as Triggered by the N214A Mutation on the Extra Domain
Authors: Shi, J.H. / Song, J.X.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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)67,6672
Polymers67,6672
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-10 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)52.495, 96.485, 68.084
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33833.613 Da / Num. of mol.: 2 / Mutation: N214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Gene: main protease / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG 6000, 0.1M Mes , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→66.678 Å / Num. all: 29514 / Num. obs: 29494 / % possible obs: 99.9 % / Redundancy: 5.73 % / Rmerge(I) obs: 0.111 / Rsym value: 0.086 / Net I/σ(I): 9.78
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.4269 / Mean I/σ(I) obs: 1.95 / Num. unique all: 3511 / Rsym value: 0.5049 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASESphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 2H2Z
Resolution: 2.3→66.478 Å / SU ML: 0.34 / σ(F): 0.09 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 1894 6.78 %
Rwork0.1959 --
obs0.2001 27953 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.675 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso mean: 26.167 Å2
Baniso -1Baniso -2Baniso -3
1-3.964 Å2-0 Å25.735 Å2
2--3.049 Å20 Å2
3----7.013 Å2
Refinement stepCycle: LAST / Resolution: 2.3→66.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 0 302 4997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054800
X-RAY DIFFRACTIONf_angle_d0.9846521
X-RAY DIFFRACTIONf_dihedral_angle_d15.9251696
X-RAY DIFFRACTIONf_chiral_restr0.064736
X-RAY DIFFRACTIONf_plane_restr0.004846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35760.3241230.26091675X-RAY DIFFRACTION86
2.3576-2.42130.31441250.24861736X-RAY DIFFRACTION88
2.4213-2.49260.35891270.24861761X-RAY DIFFRACTION89
2.4926-2.5730.32251300.23111750X-RAY DIFFRACTION92
2.573-2.6650.30171290.21911796X-RAY DIFFRACTION92
2.665-2.77170.30091360.21181856X-RAY DIFFRACTION94
2.7717-2.89780.2881340.20281878X-RAY DIFFRACTION96
2.8978-3.05060.27881380.20441905X-RAY DIFFRACTION97
3.0506-3.24170.26521390.1991927X-RAY DIFFRACTION98
3.2417-3.4920.24921400.17651924X-RAY DIFFRACTION98
3.492-3.84340.21811410.1691951X-RAY DIFFRACTION99
3.8434-4.39950.21921440.14941960X-RAY DIFFRACTION100
4.3995-5.54240.18161420.14631962X-RAY DIFFRACTION99
5.5424-66.50610.21511460.17211978X-RAY DIFFRACTION98

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