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- PDB-8aj1: SARS-CoV-2 Mpro in Complex with RK-107 -

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Basic information

Entry
Database: PDB / ID: 8aj1
TitleSARS-CoV-2 Mpro in Complex with RK-107
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN / Inhibitor complex / SARS-CoV-2
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase 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 / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane
Similarity search - Function
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. ...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. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJul 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0892
Polymers33,5501
Non-polymers5391
Water39622
1
A: 3C-like proteinase nsp5
hetero molecules

A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1784
Polymers67,1002
Non-polymers1,0772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5000 Å2
ΔGint-20 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.234, 52.955, 45.707
Angle α, β, γ (deg.)90.000, 102.806, 90.000
Int Tables number5
Space group name H-MC121

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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: 33550.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-A1IMU / (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(phenylcarbamoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide


Mass: 538.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M PCTP pH7.0, 25% w/vPEG 1500

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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: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→47.793 Å / Num. obs: 8125 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.996 / Net I/σ(I): 7.1
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 825 / CC1/2: 0.508 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.793 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 26.426 / SU ML: 0.494 / Cross valid method: FREE R-VALUE / ESU R Free: 0.408
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2745 397 4.887 %
Rwork0.1953 7727 -
all0.2 --
obs-8124 98.246 %
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: 69.138 Å2
Baniso -1Baniso -2Baniso -3
1-6.333 Å20 Å21.274 Å2
2--0.377 Å20 Å2
3----6.607 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 39 22 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0112442
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162261
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.6553319
X-RAY DIFFRACTIONr_angle_other_deg0.3811.5725194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.445303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.0326.94418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70210385
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg3.205101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.96910108
X-RAY DIFFRACTIONr_chiral_restr0.0490.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_nbd_refined0.2240.2479
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.22259
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21191
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.217
X-RAY DIFFRACTIONr_nbd_other0.1960.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.210
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_mcbond_it4.4356.7881215
X-RAY DIFFRACTIONr_mcbond_other4.4316.7891215
X-RAY DIFFRACTIONr_mcangle_it6.76912.1941517
X-RAY DIFFRACTIONr_mcangle_other6.76812.1961518
X-RAY DIFFRACTIONr_scbond_it4.7287.2281227
X-RAY DIFFRACTIONr_scbond_other4.7277.2281228
X-RAY DIFFRACTIONr_scangle_it7.55513.1371799
X-RAY DIFFRACTIONr_scangle_other7.55313.1351800
X-RAY DIFFRACTIONr_lrange_it10.8266.6562637
X-RAY DIFFRACTIONr_lrange_other10.81966.6562637
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
2.6-2.6670.456230.3745790.3776080.8230.87899.01320.36
2.667-2.740.431290.3615450.3645800.8850.88298.96550.353
2.74-2.8190.392260.3525580.3535890.8960.88999.15110.329
2.819-2.9060.339280.2915060.2945430.9070.92198.34250.269
2.906-3.0010.376320.2784980.2835350.8750.93199.06540.261
3.001-3.1060.298230.2465040.2485360.910.9598.32090.224
3.106-3.2220.254270.2254700.2265040.9380.96198.61110.204
3.222-3.3530.381180.2284590.2354860.910.96498.14810.204
3.353-3.5020.281230.2054300.2094770.9560.97194.96860.181
3.502-3.6720.354200.1694130.1784440.9380.9897.52250.151
3.672-3.8690.232230.1643940.1674240.9690.98398.34910.153
3.869-4.1020.377150.1553770.1633970.9050.98698.74060.151
4.102-4.3830.15170.1573590.1563770.9840.98699.73470.151
4.383-4.7310.225240.1723260.1763550.9720.98198.59150.168
4.731-5.1770.472170.1553070.1683310.8610.98597.88520.15
5.177-5.780.208180.1762750.1793010.9790.98497.34220.167
5.78-6.6580.29350.1562450.1582600.9740.98896.15380.152
6.658-8.1150.275120.1592070.1672280.9560.98796.05260.159
8.115-11.3140.212120.1271700.1351820.9840.9891000.135
11.314-47.7930.12250.221050.2151110.9930.97299.09910.226

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