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- PDB-2v6n: Crystal structures of the SARS-coronavirus main proteinase inacti... -

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Basic information

Entry
Database: PDB / ID: 2v6n
TitleCrystal structures of the SARS-coronavirus main proteinase inactivated by benzotriazole compounds
ComponentsREPLICASE POLYPROTEIN 1AB
KeywordsVIRAL PROTEIN / THIOL PROTEASE / RNA REPLICATION / MAIN PROTEINASE / RIBOSOMAL FRAMESHIFT / SARS / PROTEASE / HYDROLASE / POLYPROTEIN
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / suppression by virus of host type I interferon production / positive stranded viral RNA replication / protein K48-linked deubiquitination / : ...cysteine-type deubiquitinase activity => GO:0004843 / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / suppression by virus of host type I interferon production / positive stranded viral RNA replication / protein K48-linked deubiquitination / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / : / protein K63-linked deubiquitination / 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 / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / viral transcription / protein autoprocessing / 7-methylguanosine mRNA capping / host cell membrane / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / 5'-3' DNA helicase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / membrane => GO:0016020 / Hydrolases; Acting on ester bonds / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / protein dimerization activity / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / 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 / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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 / : / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / 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 Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / 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.
Similarity search - Domain/homology
4-(DIMETHYLAMINO)BENZOIC ACID / Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHUMAN SARS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
DepositionJul 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 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: REPLICASE POLYPROTEIN 1AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3334
Polymers33,8771
Non-polymers4563
Water6,503361
1
A: REPLICASE POLYPROTEIN 1AB
hetero molecules

A: REPLICASE POLYPROTEIN 1AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6668
Polymers67,7532
Non-polymers9136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2710 Å2
ΔGint-11.3 kcal/mol
Surface area32690 Å2
MethodPQS
Unit cell
Length a, b, c (Å)108.265, 81.974, 53.418
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1006-

HOH

21A-1131-

HOH

31A-1158-

HOH

41A-1329-

HOH

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Components

#1: Protein REPLICASE POLYPROTEIN 1AB / PP1AB / ORF1AB POLYPROTEIN


Mass: 33876.637 Da / Num. of mol.: 1 / Fragment: SARS-COV MAIN PROTEINASE, RESIDUES 3241-3546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6WGN0, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-XP1 / 4-(DIMETHYLAMINO)BENZOIC ACID


Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsUPON BINDING TO THE MAIN PROTEINASE, THE NUCLEOPHILE CYS145 ATTACKS THE INHIBITOR 1-(4- ...UPON BINDING TO THE MAIN PROTEINASE, THE NUCLEOPHILE CYS145 ATTACKS THE INHIBITOR 1-(4-DIMETHYLAMINOBENZOYLOXY)-BENZOTRIAZOLE (XP-59), RESULTING IN THE 4-(DIMETHYLAMINO)BENZOYL MOIETY (XP1) COVALENTLY BOUND TO THE ENZYME.

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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: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 6 / Details: 6-8% PEG6000, 0.1 M MES PH 6.0, 3% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 26, 2006 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 1.95→65 Å / Num. obs: 30270 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 27.95 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.4 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UJ1 CHAIN A

1uj1


Resolution: 1.98→64.55 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.248 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1528 5 %RANDOM
Rwork0.164 ---
obs0.166 28753 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å21.45 Å2
2--1.18 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.98→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 28 361 2760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.963389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36224.464112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2571512
X-RAY DIFFRACTIONr_chiral_restr0.1680.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21079
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21690
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4031.51582
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12422489
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.40631046
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7054.5894
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 84
Rwork0.197 1571
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)
14.94110.8577-0.77811.50590.49340.41360.2236-0.20630.13420.0421-0.08020.1202-0.10810.2862-0.1434-0.0073-0.013-0.00570.0083-0.0297-0.036213.2287-36.3857-22.8553
21.36480.2294-0.49090.4532-0.03560.2596-0.00730.0157-0.0838-0.0004-0.00380.01140.0588-0.03350.011-0.0272-0.0251-0.0117-0.0183-0.0083-0.0212-14.0576-56.5051-18.609
30.37960.1494-0.19210.52450.23610.42080.0282-0.0254-0.02950.0235-0.0361-0.01780.0089-0.02340.0079-0.0292-0.0132-0.0194-0.00570.0038-0.025-4.3312-43.3456-16.3976
47.26943.20232.04553.01740.83470.5783-0.1691-0.15770.3526-0.07510.01240.3084-0.1241-0.01220.1566-0.02190.0054-0.01170.00450.0044-0.0423-10.9556-29.5488-13.6446
50.71510.0398-0.0670.6702-0.04350.24860.037-0.07340.01580.0686-0.0233-0.0298-0.04240.0384-0.0137-0.0291-0.0284-0.011-0.0004-0.014-0.029113.7984-23.1929-7.3496
61.07440.26-0.1150.9330.2120.08910.06190.00140.0153-0.0494-0.0442-0.01520.00350.0558-0.0177-0.0269-0.0157-0.00580.00410.0015-0.050314.6469-27.044-16.9729
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 98
3X-RAY DIFFRACTION3A99 - 188
4X-RAY DIFFRACTION4A189 - 200
5X-RAY DIFFRACTION5A201 - 269
6X-RAY DIFFRACTION6A270 - 306

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