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

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Basic information

Entry
Database: PDB / ID: 8bfq
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 / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / mRNA guanylyltransferase activity / 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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / mRNA guanylyltransferase activity / 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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / 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 / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 / lyase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / copper ion binding / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / viral translational frameshifting / 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
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / 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. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-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 Nsp3 ectodomain (3Ecto) 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: 1.863 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-15 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.873, 53.629, 114.688
Angle α, β, γ (deg.)90.000, 100.827, 90.000
Int Tables number4
Space group name H-MP1211

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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: 33825.547 Da / Num. of mol.: 2
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.: 258 / 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 Å3/Da / Density % sol: 38.61 %
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: 1.86→38.68 Å / Num. obs: 43744 / % possible obs: 97.1 % / Redundancy: 5.92 % / CC1/2: 0.998 / Net I/σ(I): 10.06
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 5.64 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 6693 / CC1/2: 0.595 / % possible all: 92.5

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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: 1.863→38.68 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: FREE R-VALUE / ESU R: 0.181 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 2105 4.906 %
Rwork0.1922 40801 -
all0.195 --
obs-42906 95.254 %
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: 38.503 Å2
Baniso -1Baniso -2Baniso -3
1-0.689 Å2-0 Å20.194 Å2
2---0.532 Å20 Å2
3----0.215 Å2
Refinement stepCycle: LAST / Resolution: 1.863→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 0 258 4994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0114842
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164304
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6436582
X-RAY DIFFRACTIONr_angle_other_deg0.8621.55610032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6945610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.16522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87910776
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.76110220
X-RAY DIFFRACTIONr_chiral_restr0.0730.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025548
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02972
X-RAY DIFFRACTIONr_nbd_refined0.2270.2901
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2260.24242
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22424
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4140.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.222
X-RAY DIFFRACTIONr_nbd_other0.2310.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.213
X-RAY DIFFRACTIONr_mcbond_it3.6163.8812446
X-RAY DIFFRACTIONr_mcbond_other3.6123.8812446
X-RAY DIFFRACTIONr_mcangle_it4.8475.8083054
X-RAY DIFFRACTIONr_mcangle_other4.8485.8113055
X-RAY DIFFRACTIONr_scbond_it4.7344.3632396
X-RAY DIFFRACTIONr_scbond_other4.7314.3612395
X-RAY DIFFRACTIONr_scangle_it6.7876.3453528
X-RAY DIFFRACTIONr_scangle_other6.7866.3473529
X-RAY DIFFRACTIONr_lrange_it8.75758.2025348
X-RAY DIFFRACTIONr_lrange_other8.75457.3885305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.863-1.9120.5221050.4482343X-RAY DIFFRACTION74.3621
1.912-1.9640.3591370.3542576X-RAY DIFFRACTION83.8899
1.964-2.0210.3051210.2582910X-RAY DIFFRACTION97.2409
2.021-2.0830.3151680.2682783X-RAY DIFFRACTION97.3606
2.083-2.1510.2681400.2222774X-RAY DIFFRACTION97.6542
2.151-2.2260.2731410.2262638X-RAY DIFFRACTION97.543
2.226-2.310.3031110.2352530X-RAY DIFFRACTION96.5984
2.31-2.4040.3081470.2052455X-RAY DIFFRACTION98.0777
2.404-2.510.2661440.1952365X-RAY DIFFRACTION98.2381
2.51-2.6320.2971500.1972252X-RAY DIFFRACTION98.2011
2.632-2.7740.281370.1832154X-RAY DIFFRACTION98.58
2.774-2.9410.2241050.1762059X-RAY DIFFRACTION98.6326
2.941-3.1430.211740.1731977X-RAY DIFFRACTION98.4165
3.143-3.3930.248760.1761827X-RAY DIFFRACTION99.063
3.393-3.7140.23930.1721686X-RAY DIFFRACTION98.9433
3.714-4.1470.239980.171494X-RAY DIFFRACTION98.6981
4.147-4.780.186500.1451350X-RAY DIFFRACTION98.0392
4.78-5.8320.204590.171169X-RAY DIFFRACTION99.4332
5.832-8.1550.269340.201895X-RAY DIFFRACTION97.584
8.155-38.680.191150.18564X-RAY DIFFRACTION98.9744

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