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- PDB-9f2v: Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR02 -

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Entry
Database: PDB / ID: 9f2v
TitleCrystal structure of SARS-CoV-2 Mpro in complex with RHTCR02
Components3C-like proteinase nsp5
KeywordsANTIVIRAL PROTEIN / Complex
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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...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 / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 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 / 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 / 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 / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / 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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsEl kilani, H. / Hilgenfeld, R.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European CommissionEuropean Union
CitationJournal: J.Med.Chem. / Year: 2025
Title: Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Roske, J. / Zhang, K. / Gohl, M. / Arisetti, N. / Marsh, G.P. / Maple, H.J. / Cooper, M.S. / Karadogan, B. / Jochmans, D. / Neyts, J. / Rox, K. / ...Authors: Akula, R.K. / El Kilani, H. / Metzen, A. / Roske, J. / Zhang, K. / Gohl, M. / Arisetti, N. / Marsh, G.P. / Maple, H.J. / Cooper, M.S. / Karadogan, B. / Jochmans, D. / Neyts, J. / Rox, K. / Hilgenfeld, R. / Bronstrup, M.
History
DepositionApr 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6984
Polymers67,6512
Non-polymers1,0472
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-13 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.852, 63.688, 103.506
Angle α, β, γ (deg.)90.000, 91.171, 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
Gene: rep, 1a-1b / Production host: Escherichia coli B (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1H9E / ~{tert}-butyl ~{N}-[1-[(2~{S})-1-[[(2~{R},3~{S})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-5-fluoranyl-2-oxidanylidene-pyridin-3-yl]carbamate


Mass: 523.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34FN5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis Tris Propane pH 7.50, 2M Sodium nitrate, 20% w/vPEG 3350 and 10% v/vEthylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.191→45.884 Å / Num. obs: 208789 / % possible obs: 98.79 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08664 / Net I/σ(I): 19.9
Reflection shellResolution: 2.191→2.27 Å / Num. unique obs: 2890 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.191→45.884 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.816 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.27 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2091 1498 4.918 %
Rwork0.1667 28962 -
all0.169 --
obs-30460 98.768 %
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: 23.194 Å2
Baniso -1Baniso -2Baniso -3
1--1.203 Å20 Å20.394 Å2
2--0.634 Å2-0 Å2
3---0.552 Å2
Refinement stepCycle: LAST / Resolution: 2.191→45.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 74 111 4899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124899
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164533
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.6756664
X-RAY DIFFRACTIONr_angle_other_deg0.7231.5910412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4745608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.006522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41210773
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.765102
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.32910218
X-RAY DIFFRACTIONr_chiral_restr0.1540.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021159
X-RAY DIFFRACTIONr_nbd_refined0.2080.2858
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24276
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22450
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22611
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2140
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.25
X-RAY DIFFRACTIONr_nbd_other0.1970.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0880.22
X-RAY DIFFRACTIONr_mcbond_it1.9852.1632438
X-RAY DIFFRACTIONr_mcbond_other1.9832.1642438
X-RAY DIFFRACTIONr_mcangle_it3.083.8713044
X-RAY DIFFRACTIONr_mcangle_other3.083.8733045
X-RAY DIFFRACTIONr_scbond_it2.92.5232461
X-RAY DIFFRACTIONr_scbond_other2.8992.5232462
X-RAY DIFFRACTIONr_scangle_it4.6564.4713614
X-RAY DIFFRACTIONr_scangle_other4.6554.4713615
X-RAY DIFFRACTIONr_lrange_it6.30420.4255197
X-RAY DIFFRACTIONr_lrange_other6.30320.4225192
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
2.191-2.2480.2371110.18519860.18822360.9650.97993.78350.17
2.248-2.3090.2591180.17720900.18122120.9590.98299.81920.17
2.309-2.3760.229970.17420470.17721490.9660.98299.76730.168
2.376-2.4490.237890.16819770.17120770.9610.98499.47040.163
2.449-2.5290.223920.16219410.16520420.9730.98499.55920.158
2.529-2.6180.21930.15218140.15419270.9720.98698.96210.149
2.618-2.7160.2361090.17317520.17719040.9660.98297.74160.17
2.716-2.8270.2341030.17716830.18117880.960.98199.88810.18
2.827-2.9520.251690.17416830.17717590.9640.98199.60210.177
2.952-3.0950.217780.16515940.16816810.9750.98399.46460.171
3.095-3.2620.238720.15715270.16116070.9660.98599.50220.164
3.262-3.4590.2031010.1613710.16314800.9740.98599.45950.168
3.459-3.6960.183800.15813350.1614330.980.98798.74390.169
3.696-3.990.205690.1712170.17213240.9770.98497.12990.182
3.99-4.3670.174570.15111650.15212220.9840.9871000.168
4.367-4.8770.127440.14610720.14511160.990.9891000.168
4.877-5.6210.194390.1759380.1769850.9790.98599.18780.196
5.621-6.8590.29310.2017790.2048320.9670.9897.35580.219
6.859-9.5940.182270.1576190.1586610.9840.98997.73070.176
9.594-45.8840.145190.2173720.2133960.9890.97298.73740.25

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