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- PDB-2vj1: A Structural View of the Inactivation of the SARS-Coronavirus Mai... -

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Entry
Database: PDB / ID: 2vj1
TitleA Structural View of the Inactivation of the SARS-Coronavirus Main Proteinase by Benzotriazole Esters
ComponentsSARS CORONAVIRUS MAIN PROTEINASE
KeywordsHYDROLASE / SARS / PROTEASE / POLYPROTEIN / THIOL PROTEASE / RIBOSOMAL FRAMESHIFT / SARS CORONAVIRUS MAIN PROTEINASE
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / viral transcription / SARS-CoV-1 modulates host translation machinery / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane
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 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) 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 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Trypsin-like serine proteases / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7
Similarity search - Domain/homology
BENZOIC ACID / 4-(DIMETHYLAMINO)BENZOIC ACID / Orf1a polyprotein / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHUMAN SARS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsVerschueren, K.H.G. / Pumpor, K. / Anemueller, S. / Mesters, J.R. / Hilgenfeld, R.
CitationJournal: Chem.Biol. / Year: 2008
Title: A Structural View of the Inactivation of the Sars Coronavirus Main Proteinase by Benzotriazole Esters.
Authors: Verschueren, K.H.G. / Pumpor, K. / Anemueller, S. / Chen, S. / Mesters, J.R. / Hilgenfeld, R.
History
DepositionDec 6, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionJul 1, 2008ID: 2CGG
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

Downloads & links

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Assembly

Deposited unit
A: SARS CORONAVIRUS MAIN PROTEINASE
B: SARS CORONAVIRUS MAIN PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2087
Polymers68,6862
Non-polymers5225
Water5,441302
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-22 kcal/mol
Surface area30630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)52.231, 97.760, 67.709
Angle α, β, γ (deg.)90.00, 103.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SARS CORONAVIRUS MAIN PROTEINASE


Mass: 34343.129 Da / Num. of mol.: 2 / Fragment: RESIDUES 3242-3544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: A7J8L3, UniProt: P0C6X7*PLUS, EC: 3.4.34.-
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-XP1 / 4-(DIMETHYLAMINO)BENZOIC ACID


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / 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: 2.5 Å3/Da / Density % sol: 50.2 % / Description: NONE
Crystal growpH: 6.5
Details: 5% PEG10000, 0.1M MES PH6.5, 3% ETHYLNE GLYCOL, 50MM NH4-ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8157
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 7, 2005 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 2.25→39.27 Å / Num. obs: 31422 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.91 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJ1

1uj1


Resolution: 2.25→65.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.502 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1575 5 %RANDOM
Rwork0.183 ---
obs0.187 29847 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å21.28 Å2
2--0.84 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.25→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 29 302 4983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224845
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9536586
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5185613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73224.292219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44415787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6081525
X-RAY DIFFRACTIONr_chiral_restr0.1070.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023705
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.22167
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23245
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8671.53077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48124872
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17331988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1714.51708
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: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 102
Rwork0.237 2213
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
131.396519.1582-13.810416.758-13.082310.351-1.02570.1294-3.7348-0.9618-0.7414-1.44770.3738-0.43041.767100.0560.1746-0.1205-0.01020.4584-14.7183-7.991924.3341
21.9794-0.192-1.38593.51361.3932.47310.3460.11350.3668-0.8171-0.0245-0.327-0.8035-0.048-0.32150.1833-0.00510.1105-0.17730.01650.0113-4.771423.511317.4577
31.7725-0.953-0.88613.66991.45412.24970.13350.0678-0.0139-0.3039-0.0227-0.0838-0.2526-0.0226-0.1108-0.0575-0.0242-0.0071-0.13730.0169-0.075-4.28797.186217.2176
42.33756.4137-2.494626.0876-10.797513.736-0.18090.18190.1904-2.91180.58030.39420.1367-0.172-0.39940.3313-0.01010.0654-0.109-0.0209-0.04890.35110.32824.179
52.81861.4558-2.0152.8668-2.76683.6531-0.3809-0.0384-0.2443-0.35470.0508-0.20070.48810.10870.33-0.0575-0.02790.02-0.1513-0.00020.0031.7083-19.950820.399
64.35142.03860.51547.0451-1.89834.3403-0.07470.2850.13160.02980.15390.75790.1484-0.6584-0.0792-0.1621-0.0205-0.0249-0.09110.0149-0.0342-7.7853-16.224519.8816
730.80752.7199.66852.9091-2.04226.17550.82942.8444-0.9884-0.5322-0.5644-0.8577-0.58870.0955-0.265-0.06520.0108-0.07180.1897-0.0886-0.0548-16.5305-0.741214.8189
83.14751.7423-1.17441.7653-1.56564.19520.277-0.93220.25840.3281-0.24220-0.4257-0.3462-0.0348-0.128-0.0269-0.00040.2746-0.0912-0.1835-28.50040.289745.8922
93.60341.52961.29592.4697-0.5063.79830.064-0.2955-0.07260.0419-0.0898-0.09480.0508-0.2540.0258-0.1415-0.0225-0.0174-0.01-0.0157-0.1208-28.0215-3.76629.8549
104.06390.3978-5.59061.5696-9.11355.6248-0.4649-0.3896-0.5505-0.38080.14420.29414.4562-0.26650.32070.6055-0.00980.02590.18430.00420.1315-31.9523-17.980126.1493
116.50070.3496-2.04262.8218-0.06243.7713-0.06810.87870.1225-0.12850.17810.0613-0.0302-0.1801-0.11-0.1526-0.0246-0.02380.1120.0086-0.1863-31.2759-7.84272.1272
124.7496-0.2172-1.46063.24590.06244.6452-0.0520.3927-0.00230.06720.0646-0.4244-0.06230.3183-0.0127-0.1634-0.0486-0.04810.0579-0.0003-0.1438-22.4552-7.44927.232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 7
2X-RAY DIFFRACTION2A8 - 98
3X-RAY DIFFRACTION3A99 - 188
4X-RAY DIFFRACTION4A189 - 200
5X-RAY DIFFRACTION5A201 - 269
6X-RAY DIFFRACTION6A270 - 301
7X-RAY DIFFRACTION7B2 - 7
8X-RAY DIFFRACTION8B8 - 98
9X-RAY DIFFRACTION9B99 - 188
10X-RAY DIFFRACTION10B189 - 200
11X-RAY DIFFRACTION11B201 - 269
12X-RAY DIFFRACTION12B270 - 301

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