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- PDB-8drt: Product structure of SARS-CoV-2 Mpro C145A mutant in complex with... -

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Basic information

Entry
Database: PDB / ID: 8drt
TitleProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence (form 2)
Components3C-like proteinase nsp5
KeywordsHYDROLASE / Viral protease / SARS-CoV-2
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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / 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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / host cell endosome / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / symbiont-mediated degradation of host mRNA / forked DNA-dependent helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / four-way junction helicase activity / 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 / 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 / host cell perinuclear region of cytoplasm / regulation of autophagy / 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
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. ...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 / : / 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
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Paetzel, M. / Strynadka, N.C.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2022
Title: X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.
Authors: Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Gentile, F. / Ton, A.T. / Ng, M. / Cherkasov, A. / Strynadka, N.C.J. / Paetzel, M.
History
DepositionJul 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3C-like proteinase nsp5
A: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)67,6032
Polymers67,6032
Non-polymers00
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-10 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.856, 105.078, 52.290
Angle α, β, γ (deg.)90.000, 104.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33801.566 Da / Num. of mol.: 2 / Fragment: UNP residues 3264-3563 / Mutation: C145A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 20% PEG3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2021
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.26→105.08 Å / Num. obs: 79812 / % possible obs: 68 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Χ2: 0.95 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→45.61 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 21.52 / Num. unique obs: 75618 / CC1/2: 0.995 / Rpim(I) all: 0.026 / % possible all: 94.74

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7JOY

7joy


Resolution: 1.5→50.63 Å / SU ML: 0.1333 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.3699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1827 3798 5.02 %
Rwork0.1546 71818 -
obs0.156 75616 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 0 603 5324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00654893
X-RAY DIFFRACTIONf_angle_d0.94526674
X-RAY DIFFRACTIONf_chiral_restr0.0611763
X-RAY DIFFRACTIONf_plane_restr0.006870
X-RAY DIFFRACTIONf_dihedral_angle_d13.11161768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.24941230.18592009X-RAY DIFFRACTION73.54
1.52-1.540.2261330.17952400X-RAY DIFFRACTION84.46
1.54-1.560.20961200.17042603X-RAY DIFFRACTION93.51
1.56-1.580.19011380.16222672X-RAY DIFFRACTION94.42
1.58-1.610.19831430.16662620X-RAY DIFFRACTION94.98
1.61-1.630.18631380.16082689X-RAY DIFFRACTION95.54
1.63-1.660.2111420.16042651X-RAY DIFFRACTION95.19
1.66-1.690.18561330.16372719X-RAY DIFFRACTION96.16
1.69-1.720.20031570.16242633X-RAY DIFFRACTION95.16
1.72-1.750.20491330.16292721X-RAY DIFFRACTION96.52
1.75-1.790.21321490.17052653X-RAY DIFFRACTION95.66
1.79-1.820.20091320.17392719X-RAY DIFFRACTION96.48
1.82-1.870.16071220.17862714X-RAY DIFFRACTION94.94
1.87-1.910.22051340.17122532X-RAY DIFFRACTION90.9
1.91-1.970.19111400.16112736X-RAY DIFFRACTION97.82
1.97-2.020.20491330.16332754X-RAY DIFFRACTION97.01
2.02-2.090.19181610.16632709X-RAY DIFFRACTION96.73
2.09-2.160.19671480.16122707X-RAY DIFFRACTION97.47
2.16-2.250.19261460.15632733X-RAY DIFFRACTION97.46
2.25-2.350.18771550.16412743X-RAY DIFFRACTION97.58
2.35-2.480.18391350.16622727X-RAY DIFFRACTION97.08
2.48-2.630.19931410.16252690X-RAY DIFFRACTION95.16
2.63-2.830.20791320.172672X-RAY DIFFRACTION94.73
2.83-3.120.19291580.15332775X-RAY DIFFRACTION98.72
3.12-3.570.17161590.14122770X-RAY DIFFRACTION98.82
3.57-4.50.1461630.12342750X-RAY DIFFRACTION97.72
4.5-50.630.14781300.13982717X-RAY DIFFRACTION94.15
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)
12.17082643637-0.912159763402-1.021189416331.602851879180.3096561960282.10867509480.07287504022210.04571379760210.104355775062-0.141070260808-0.0436659453533-0.216373353046-0.003658054516880.252500678613-0.03321813693650.106394979154-0.0089584916856-0.008637166950690.09724511642720.01215224257320.12860731715323.160355206542.99986265822.77293878236
21.23873839824-0.139903192369-0.8727504597712.99626467524-1.443430674034.94954927633-0.168451558542-0.136802864337-0.332037758317-0.0746911523907-0.196661561372-0.4098296000140.4045235909980.5923458958170.2897973743730.1852123157960.05044163022990.03151135691630.1939037264230.02248751728890.32035172872829.173788980432.45598059531.09697167311
31.04183383407-0.134837041822-0.2936098145041.41516119878-0.05287662761521.27992161398-0.01738454511020.0488167707437-0.0228494100148-0.02819265669790.03995363944710.05280798915730.0148153182773-0.0167648694248-0.02609624347680.0745638134156-0.00659050853135-0.01209203394190.0630509364594-0.002975763035510.1014696405415.145377618646.82167344482.71463418884
41.74216679198-0.157748810381-0.4292333917781.638547757590.06601793828811.080930815180.0822668014020.05979139529650.294351628665-0.0180166266607-0.0234972660161-0.242986415853-0.1329127651830.0857520983778-0.05022660145880.124626074477-0.0224869771075-0.002005771359590.08978377269790.01670243869370.16875986903121.743347761357.4639189272-2.84497466658
52.408006482380.23542696935-0.09905494272693.29320842941-1.414833394842.375558102770.0166128577260.07882077529780.0806916321662-0.0549360526278-0.006359755347960.0603031677787-0.100459968739-0.0131943015296-0.007185391394510.1282418200520.0122593110673-0.02149753289290.0638311894652.43507299945E-50.138382336825-4.0943875354270.82209506581.42159712346
62.639807032951.811022519870.3234124341392.38191307356-0.05701265008051.295045684550.0683711960618-0.181613228687-0.02063327020410.115792448123-0.0969599132546-0.0349881304904-0.0252354737366-0.02433461696240.01727933219090.1275920322260.0233837151471-0.01308351615550.1094801020090.004546180544430.131409220254-2.0653250153462.39042744869.13940742339
73.318422248221.18599412164-1.28791988780.737257591558-0.4501600269311.44843528609-0.08629171149890.1460512636810.0066296667476-0.03130294877640.08279816263960.06547228999480.106864631852-0.2100250306230.01002514229440.104358537084-0.0115333999007-0.02493769591040.1141675854110.009702962247270.108781780888-2.6749011798240.529618534521.063638459
82.86266358594-2.66789767539-0.9031466892525.91556601119-0.1726958975031.95086629416-0.0330799826397-0.123873505609-0.0252993363259-0.004978056509670.1339150800260.422609643157-0.0392147861303-0.347503433498-0.09866084900610.18989024106-0.0363813659433-0.01356107039920.3240575961780.02411652843170.264248202372-21.656562486739.208807468829.7240470046
91.379312816930.594530734801-0.2652956133741.44959832007-0.1123841355041.23478954227-0.02258019048860.004990551666430.02840536262520.02516152165720.05602203063280.01666534196770.0317676806172-0.134571392524-0.02276770035270.09002605565760.00162206066506-0.0127222319860.1154395433310.007420370629140.123405438997-2.6998710476545.184329775626.3140042784
101.66114860241-0.417754761294-0.1149792986511.394707565330.3239933428992.11867738545-0.0360683246533-0.0145401549930.1324613340230.0455980312292-0.00762132244483-0.0242379221043-0.2826411667920.05791949999740.03092841663360.135666388859-0.0175732223794-0.02080848868820.08178009653140.002461742202430.12681752809318.621336514866.50478614127.495303475
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 59 )AB1 - 591 - 59
22chain 'A' and (resid 60 through 83 )AB60 - 8360 - 83
33chain 'A' and (resid 84 through 167 )AB84 - 16784 - 167
44chain 'A' and (resid 168 through 200 )AB168 - 200168 - 200
55chain 'A' and (resid 201 through 274 )AB201 - 274201 - 274
66chain 'A' and (resid 275 through 306 )AB275 - 306275 - 306
77chain 'B' and (resid 1 through 43 )BA1 - 431 - 43
88chain 'B' and (resid 44 through 66 )BA44 - 6644 - 66
99chain 'B' and (resid 67 through 200 )BA67 - 20067 - 200
1010chain 'B' and (resid 201 through 306 )BA201 - 306201 - 306

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