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- PDB-7nt2: Crystal structure of SARS CoV2 main protease in complex with FSP006 -

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Entry
Database: PDB / ID: 7nt2
TitleCrystal structure of SARS CoV2 main protease in complex with FSP006
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Protease / Complex / Covalent
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 / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / methylation / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / Coronavirus 3Ecto domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / : / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Peptidase family C16 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 Nsp4 C-terminal (Nsp4C) 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-URK / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.145 Å
AuthorsOerlemans, R. / Eris, D. / Wang, M. / Sharpe, M. / Domling, A. / Groves, M.R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Combining High-Throughput Synthesis and High-Throughput Protein Crystallography for Accelerated Hit Identification.
Authors: Sutanto, F. / Shaabani, S. / Oerlemans, R. / Eris, D. / Patil, P. / Hadian, M. / Wang, M. / Sharpe, M.E. / Groves, M.R. / Domling, A.
History
DepositionMar 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,66211
Polymers67,6512
Non-polymers1,0119
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-9 kcal/mol
Surface area25340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.155, 100.588, 104.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3C-like proteinase / 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
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, SARS coronavirus main proteinase

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Non-polymers , 5 types, 188 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-URK / [(1S)-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate / [(1~{S})-2-[(2,3-dimethoxyphenyl)methylamino]-1-(4-nitrophenyl)-2-oxidanylidene-ethyl] prop-2-enoate / FSP006


Mass: 400.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65545678 Å3/Da / Density % sol: 53.7090645 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 by adding the stock to ...Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP006 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP006 by adding the stock to crystallisation drops in a 1/10 ratio yielding 10% (V/V) final DMSO concentration.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000035 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000035 Å / Relative weight: 1
ReflectionResolution: 2.14→46.45 Å / Num. obs: 39260 / % possible obs: 98.1 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.069 / Rrim(I) all: 0.149 / Net I/σ(I): 9.8
Reflection shellResolution: 2.14→2.21 Å / Redundancy: 7.9 % / Rmerge(I) obs: 1.329 / Num. unique obs: 3188 / CC1/2: 0.634 / Rpim(I) all: 0.712 / Rrim(I) all: 1.516

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data reduction
XDSdata processing
Aimless0.7.4data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6lu7

6lu7


Resolution: 2.145→46.447 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.191 / SU B: 6.634 / SU ML: 0.162 / Average fsc free: 0.8839 / Average fsc work: 0.8977 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 1962 5.003 %RANDOM
Rwork0.2019 37258 --
all0.204 ---
obs-39220 97.657 %-
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: 40.003 Å2
Baniso -1Baniso -2Baniso -3
1--2.693 Å2-0 Å20 Å2
2--2.82 Å2-0 Å2
3----0.127 Å2
Refinement stepCycle: LAST / Resolution: 2.145→46.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4681 0 61 179 4921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134878
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174393
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6396626
X-RAY DIFFRACTIONr_angle_other_deg1.2911.56810195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9425611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3523.21243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94215775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8761522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021020
X-RAY DIFFRACTIONr_nbd_refined0.1990.2851
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24132
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22327
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2185
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.215
X-RAY DIFFRACTIONr_nbd_other0.2190.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.28
X-RAY DIFFRACTIONr_mcbond_it3.1094.1152438
X-RAY DIFFRACTIONr_mcbond_other3.1024.1142437
X-RAY DIFFRACTIONr_mcangle_it4.6626.1573051
X-RAY DIFFRACTIONr_mcangle_other4.6616.1583052
X-RAY DIFFRACTIONr_scbond_it3.7364.5232440
X-RAY DIFFRACTIONr_scbond_other3.7354.5252441
X-RAY DIFFRACTIONr_scangle_it5.546.6243575
X-RAY DIFFRACTIONr_scangle_other5.5396.6263576
X-RAY DIFFRACTIONr_lrange_it7.81248.0865176
X-RAY DIFFRACTIONr_lrange_other7.78348.0465154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.145-2.20.3341430.2992725X-RAY DIFFRACTION98.3539
2.2-2.260.3321410.2792690X-RAY DIFFRACTION99.438
2.26-2.3260.2971380.282615X-RAY DIFFRACTION99.243
2.326-2.3970.3151330.2622514X-RAY DIFFRACTION98.4015
2.397-2.4760.3011290.2392441X-RAY DIFFRACTION98.6943
2.476-2.5620.2891230.242334X-RAY DIFFRACTION96.9996
2.562-2.6590.2681180.2132255X-RAY DIFFRACTION96.6599
2.659-2.7670.3091190.2032215X-RAY DIFFRACTION98.7727
2.767-2.8890.281090.212101X-RAY DIFFRACTION98.2222
2.889-3.030.2721090.2082053X-RAY DIFFRACTION98.4966
3.03-3.1930.2641020.2231933X-RAY DIFFRACTION98.3092
3.193-3.3860.277980.2281829X-RAY DIFFRACTION97.8669
3.386-3.6180.238910.211702X-RAY DIFFRACTION97.1816
3.618-3.9060.259790.1961554X-RAY DIFFRACTION94.3931
3.906-4.2760.205790.1551467X-RAY DIFFRACTION97.1716
4.276-4.7750.179680.1451344X-RAY DIFFRACTION96.4481
4.775-5.5040.206630.1541204X-RAY DIFFRACTION96.6438
5.504-6.7180.228530.2051006X-RAY DIFFRACTION95.2338
6.718-9.4020.179410.142796X-RAY DIFFRACTION93.9394

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