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- PDB-6xkh: THE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXI... -

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Basic information

Entry
Database: PDB / ID: 6xkh
TitleTHE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXIDIZED C145 (sulfinic acid cysteine)
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / 3CL main protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / 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 / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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 / : ...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 / : / Lipocalin signature. / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsTan, K. / Maltseva, N.I. / Welk, L.F. / Jedrzejczak, R.P. / Coates, L. / Kovalevsky, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: THE 1.28A CRYSTAL STRUCTURE OF 3CL MAINPRO OF SARS-COV-2 WITH OXIDIZED C145 (sulfinic acid cysteine)
Authors: Tan, K. / Maltseva, N.I. / Welk, L.F. / Jedrzejczak, R.P. / Coates, L. / Kovalevsky, A. / Joachimiak, A.
History
DepositionJun 26, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionJul 8, 2020ID: 6XG2
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2258
Polymers33,8581
Non-polymers3677
Water4,306239
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,45016
Polymers67,7152
Non-polymers73514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5720 Å2
ΔGint-9 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.650, 83.313, 54.663
Angle α, β, γ (deg.)90.000, 117.996, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-667-

HOH

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Components

#1: Protein 3C-like proteinase


Mass: 33857.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 15% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.28→34.64 Å / Num. obs: 96251 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 18.36 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.029 / Rrim(I) all: 0.066 / Χ2: 1.539 / Net I/σ(I): 40.75
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.095 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 4675 / CC1/2: 0.57 / CC star: 0.852 / Rpim(I) all: 0.627 / Rrim(I) all: 1.27 / Χ2: 0.642 / % possible all: 96.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YB7

6yb7


Resolution: 1.28→32.64 Å / SU ML: 0.1304 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 4932 5.13 %random
Rwork0.1563 91187 --
obs0.1573 96119 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.08 Å2
Refinement stepCycle: LAST / Resolution: 1.28→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 24 239 2632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872540
X-RAY DIFFRACTIONf_angle_d1.0133464
X-RAY DIFFRACTIONf_chiral_restr0.0817391
X-RAY DIFFRACTIONf_plane_restr0.0075455
X-RAY DIFFRACTIONf_dihedral_angle_d19.2533920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.33541350.31812631X-RAY DIFFRACTION85.66
1.3-1.310.31511670.31282949X-RAY DIFFRACTION96.47
1.31-1.330.29531450.27552942X-RAY DIFFRACTION93.46
1.33-1.340.26671720.27643016X-RAY DIFFRACTION98.73
1.34-1.360.2541700.26363093X-RAY DIFFRACTION99.79
1.36-1.380.2831590.25853094X-RAY DIFFRACTION99.75
1.38-1.40.2621770.24723035X-RAY DIFFRACTION99.5
1.4-1.420.29611910.23293051X-RAY DIFFRACTION99.6
1.42-1.440.23541780.22353076X-RAY DIFFRACTION99.12
1.44-1.470.23011590.2113006X-RAY DIFFRACTION98.88
1.47-1.490.24481680.19883046X-RAY DIFFRACTION98.68
1.49-1.520.21181530.18423080X-RAY DIFFRACTION97.82
1.52-1.550.22221480.18392908X-RAY DIFFRACTION95.05
1.55-1.580.16831410.17043115X-RAY DIFFRACTION99.75
1.58-1.610.20011590.17043119X-RAY DIFFRACTION99.82
1.61-1.650.19241580.17033079X-RAY DIFFRACTION99.78
1.65-1.690.15881560.16613094X-RAY DIFFRACTION99.63
1.69-1.740.19661470.16153089X-RAY DIFFRACTION99.48
1.74-1.790.19091680.16933066X-RAY DIFFRACTION99.63
1.79-1.850.20081710.16183037X-RAY DIFFRACTION98.65
1.85-1.910.18711710.16972997X-RAY DIFFRACTION96.56
1.91-1.990.15131760.15573075X-RAY DIFFRACTION98.66
1.99-2.080.15511570.15713069X-RAY DIFFRACTION99.97
2.08-2.190.15611540.15083134X-RAY DIFFRACTION99.61
2.19-2.330.16231750.14853064X-RAY DIFFRACTION99.48
2.33-2.510.17211710.14783086X-RAY DIFFRACTION99.48
2.51-2.760.1761840.15142992X-RAY DIFFRACTION97.04
2.76-3.160.15391670.14813089X-RAY DIFFRACTION99.48
3.16-3.980.16381810.13633088X-RAY DIFFRACTION98.79
3.98-32.640.1561740.13173067X-RAY DIFFRACTION97.12
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)
10.9833554967140.2399279283050.2083842255182.147640416792.09741127535.970503528550.155220832134-0.03474784036020.0852231662407-0.1315967999420.0449997826574-0.277525846934-0.3197579630710.228364465254-0.1806092887080.215028462291-0.05168646187190.06810877147070.17556449122-0.02269501371850.1857419489461.0027978948710.568483863812.592585945
22.124424873671.95096498674-0.5480346348856.90672318785-2.026558123886.733300434530.114625106944-0.333132770170.03489539228710.318857674985-0.0534120755921-0.774791029806-0.3412731487890.827569017642-0.02531459597380.238536835779-0.0815790138837-0.02495366691530.334786136001-0.130549809980.3392195895576.9054455382214.549968751828.7724227288
31.215562686340.554110292025-0.3100440167423.293566131630.4659019252552.163839923030.0655286723373-0.06674136494950.202827665119-0.1012469275830.0662785535286-0.0603615511566-0.5058045761730.0341541718874-0.08977722677240.269128959193-0.00442349924580.05879959342470.141732407697-0.0251830216680.153454434047-6.5947436608513.800732495717.2280285397
42.033912357031.08792641199-1.072382513084.734097960970.2232724240413.207804590740.02474022571020.00920468150269-0.00844987345612-0.1689331980570.0744938423798-0.244758163106-0.2264268957720.146901196759-0.06746688723760.181303402229-0.01635470202240.0185818466360.168261855956-0.02610649497320.10231237198-0.9207022710992.1527326140310.2211638431
51.100771418890.569324494170.4843174668941.886682695391.427869168434.054025299970.08020529485-0.0215877121766-0.09644526143360.1498587443790.0284021645664-0.1566040006430.2415699699960.102794036658-0.1168932397520.138577273603-0.001837716097910.009811045717520.161971480139-0.0053751190870.13676993541-5.56679105796-4.3149375675515.8276014836
62.923691003680.7083574747920.3299840659743.643141340510.9126784141564.58515719008-0.01056740103490.0723838233336-0.1632130434320.0139199721982-0.04175872599660.1848968127020.367950503823-0.4501728808190.0299855070770.231304669991-0.07857748679820.01854980647190.284826739286-0.0472583721350.135851497774-16.1392133931-15.9189375751.3932783192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 110 )
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 155 )
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 306 )

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