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- PDB-2bx3: Crystal Structure of SARS Coronavirus Main Proteinase (P43212) -

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Basic information

Entry
Database: PDB / ID: 2bx3
TitleCrystal Structure of SARS Coronavirus Main Proteinase (P43212)
ComponentsMAIN PROTEINASE
KeywordsHYDROLASE / SARS / ANTI-PARALLEL B-BARREL / ANTI-PARALLEL A- HELICES / VIRAL PROTEIN
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 / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / viral RNA-directed RNA polymerase complex ...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 / mRNA (guanine-N7-)-methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / 5'-3' RNA helicase activity / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / RNA-templated transcription / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell endoplasmic reticulum / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / positive regulation of viral genome replication / suppression by virus of host TRAF-mediated signal transduction => GO:0039527 / helicase activity / protein autoprocessing / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / DNA-templated transcription / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding
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 / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 15, middle domain, alpha/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 / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Viral (Superfamily 1) RNA helicase / Coronavirus replicase NSP15, middle domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / RNA polymerase, N-terminal, coronavirus / Non-structural protein 14, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, N-terminal oligomerization / Non-structural protein NSP15, middle domain superfamily / Nonstructural protein 15, middle domain, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / NSP1, globular domain, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / 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 replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus RNA synthesis protein NSP10 / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus replicase NSP8 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus endopeptidase C30 / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, C-terminal, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS CORONAVIRUS SIN2774
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVerschueren, K.H.G. / Mesters, J.R. / Hilgenfeld, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Ph-Dependent Conformational Flexibility of the Sars-Cov Main Proteinase (M(Pro)) Dimer: Molecular Dynamics Simulations and Multiple X-Ray Structure Analyses.
Authors: Tan, J. / Verschueren, K.H.G. / Anand, K. / Shen, J. / Yang, M. / Xu, Y. / Rao, Z. / Bigalke, J. / Heisen, B. / Mesters, J.R. / Chen, K. / Shen, X. / Jiang, H. / Hilgenfeld, R.
History
DepositionJul 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAIN PROTEINASE


Theoretical massNumber of molelcules
Total (without water)33,8771
Polymers33,8771
Non-polymers00
Water4,666259
1
A: MAIN PROTEINASE

A: MAIN PROTEINASE


Theoretical massNumber of molelcules
Total (without water)67,7532
Polymers67,7532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)69.675, 69.675, 100.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MAIN PROTEINASE


Mass: 33876.637 Da / Num. of mol.: 1 / Fragment: RESIDUES 3241-3546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS CORONAVIRUS SIN2774 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER (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.: 259 / 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: 1.8 Å3/Da / Density % sol: 30 % / Description: DATA COLLECTED TO 1.7A BUT PROCESSED TO 2A
Crystal growpH: 5.9 / Details: 15% PEG6000, 0.1M MES PH 5.9, 3% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8031
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8031 Å / Relative weight: 1
ReflectionResolution: 2→40.82 Å / Num. obs: 17333 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Biso Wilson estimate: 20.32 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJ1
Resolution: 2→56.8 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 9.262 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.244 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 884 5.1 %RANDOM
Rwork0.175 ---
obs0.18 16395 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2---1.77 Å20 Å2
3---3.54 Å2
Refinement stepCycle: LAST / Resolution: 2→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 259 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222477
X-RAY DIFFRACTIONr_bond_other_d0.0010.022184
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9483372
X-RAY DIFFRACTIONr_angle_other_deg0.81835110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2075318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60324.298114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82115410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8461513
X-RAY DIFFRACTIONr_chiral_restr0.1170.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022802
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02512
X-RAY DIFFRACTIONr_nbd_refined0.2290.3579
X-RAY DIFFRACTIONr_nbd_other0.2090.32429
X-RAY DIFFRACTIONr_nbtor_refined0.1970.51226
X-RAY DIFFRACTIONr_nbtor_other0.0990.51548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.5315
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.349
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.3124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.532
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70921905
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18332499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34721071
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9253873
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 60
Rwork0.189 1182
Refinement TLS params.Method: refined / Origin x: 6.7415 Å / Origin y: 69.1774 Å / Origin z: 12.599 Å
111213212223313233
T-0.0035 Å2-0.0107 Å20.0045 Å2--0.029 Å2-0.009 Å2---0.1226 Å2
L2.1931 °2-0.1493 °2-0.1451 °2-0.498 °2-0.1047 °2--0.39 °2
S-0.0136 Å °-0.0212 Å °-0.0045 Å °-0.019 Å °0.01 Å °0.0168 Å °0.032 Å °-0.018 Å °0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 101
2X-RAY DIFFRACTION1A102 - 184
3X-RAY DIFFRACTION1A201 - 300

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