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- PDB-8bfo: Structure of the apo form of Mpro from SARS-CoV-2 -

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Basic information

Entry
Database: PDB / ID: 8bfo
TitleStructure of the apo form of Mpro from SARS-CoV-2
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / Mpro / 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) / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMedrano, F.J. / Romero, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentPIE-202020E224 Spain
CitationJournal: Commun Chem / Year: 2024
Title: Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2.
Authors: Medrano, F.J. / de la Hoz-Rodriguez, S. / Marti, S. / Arafet, K. / Schirmeister, T. / Hammerschmidt, S.J. / Muller, C. / Gonzalez-Martinez, A. / Santillana, E. / Ziebuhr, J. / Romero, A. / ...Authors: Medrano, F.J. / de la Hoz-Rodriguez, S. / Marti, S. / Arafet, K. / Schirmeister, T. / Hammerschmidt, S.J. / Muller, C. / Gonzalez-Martinez, A. / Santillana, E. / Ziebuhr, J. / Romero, A. / Zimmer, C. / Weldert, A. / Zimmermann, R. / Lodola, A. / Swiderek, K. / Moliner, V. / Gonzalez, F.V.
History
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)33,6971
Polymers33,6971
Non-polymers00
Water1,08160
1
A: 3C-like proteinase nsp5

A: 3C-like proteinase nsp5


Theoretical massNumber of molelcules
Total (without water)67,3952
Polymers67,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3080 Å2
ΔGint-15 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.980, 53.933, 44.738
Angle α, β, γ (deg.)90.000, 101.004, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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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: 33697.418 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 BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium HEPES at pH 7.0 containing 22% PEG 4000 and 3% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.98→48.71 Å / Num. obs: 18561 / % possible obs: 98.6 % / Redundancy: 4.83 % / CC1/2: 0.987 / Net I/σ(I): 7.75
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 4.66 % / Mean I/σ(I) obs: 0.73 / Num. unique obs: 2816 / CC1/2: 0.385 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K3T

7k3t


Resolution: 1.99→48.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: FREE R-VALUE / ESU R: 0.237 / ESU R Free: 0.215
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2859 900 4.862 %
Rwork0.212 17612 -
all0.216 --
obs-18512 99.473 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.822 Å20 Å2-1.131 Å2
2--0.917 Å20 Å2
3----1.208 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 0 60 2418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0112411
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162146
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.6433277
X-RAY DIFFRACTIONr_angle_other_deg0.7331.5565001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0195304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.882511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42510386
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.30710109
X-RAY DIFFRACTIONr_chiral_restr0.0590.2370
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022759
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02485
X-RAY DIFFRACTIONr_nbd_refined0.2110.2433
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.22063
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21190
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.222
X-RAY DIFFRACTIONr_nbd_other0.2350.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.210
X-RAY DIFFRACTIONr_mcbond_it4.0055.0761219
X-RAY DIFFRACTIONr_mcbond_other3.9945.0751219
X-RAY DIFFRACTIONr_mcangle_it5.4277.5981522
X-RAY DIFFRACTIONr_mcangle_other5.4287.6011523
X-RAY DIFFRACTIONr_scbond_it4.0915.421192
X-RAY DIFFRACTIONr_scbond_other4.095.4211193
X-RAY DIFFRACTIONr_scangle_it5.8947.981755
X-RAY DIFFRACTIONr_scangle_other5.8927.9821756
X-RAY DIFFRACTIONr_lrange_it8.49473.5312618
X-RAY DIFFRACTIONr_lrange_other8.48473.5022613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.99-2.0420.543630.48612820.48913770.8830.87997.67610.496
2.042-2.0970.432650.42912550.42913210.9170.88399.92430.43
2.097-2.1580.317660.35712380.35513060.9180.91699.84690.358
2.158-2.2240.445610.35811830.36212440.8950.9181000.349
2.224-2.2970.301640.32311510.32212150.9360.9331000.301
2.297-2.3780.342530.27711180.27911720.9290.95199.91470.247
2.378-2.4670.352530.24811010.25211590.9260.9699.56860.22
2.467-2.5680.391490.27310270.27910780.9030.94999.81450.245
2.568-2.6820.341590.25910000.26310610.9190.95799.81150.229
2.682-2.8120.369530.2459630.25110180.8960.9699.80350.221
2.812-2.9640.348440.2459010.259480.9280.96499.68350.223
2.964-3.1430.302370.2128740.2159110.9260.9741000.203
3.143-3.3590.275330.1998320.2018680.9640.97799.65440.196
3.359-3.6260.309280.2047490.2087800.9550.97699.61540.203
3.626-3.970.227340.1897100.197470.9690.97899.59840.194
3.97-4.4350.279320.1556280.166640.9480.98599.39760.173
4.435-5.1140.233230.1415570.1445890.9790.98798.4720.16
5.114-6.2460.249380.1854680.195120.9760.98398.82810.207
6.246-8.7620.219280.1893660.1914010.9710.98198.25440.219
8.762-48.710.205170.1612090.1642360.9750.9895.76270.204

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