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- PDB-7nt1: Crystal structure of SARS CoV2 main protease in complex with FSP007 -

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Basic information

Entry
Database: PDB / ID: 7nt1
TitleCrystal structure of SARS CoV2 main protease in complex with FSP007
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
Chem-UQW / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,4209
Polymers67,6512
Non-polymers7697
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-7 kcal/mol
Surface area26040 Å2
Unit cell
Length a, b, c (Å)68.175, 102.171, 104.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

#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
#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-UQW / [(2R)-1-[2-(1H-indol-3-yl)ethylamino]-1-oxidanylidene-butan-2-yl] prop-2-enoate / [(2~{R})-1-[2-(1~{H}-indol-3-yl)ethylamino]-1-oxidanylidene-butan-2-yl] prop-2-enoate


Mass: 300.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68912506 Å3/Da / Density % sol: 54.2886314 %
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 FSP007 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 by adding the stock to ...Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock FSP007 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM FSP007 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: 2.85→46.48 Å / Num. obs: 17362 / % possible obs: 98.9 % / Redundancy: 4.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.135 / Rrim(I) all: 0.227 / Net I/σ(I): 6.3
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.12 / Num. unique obs: 2511 / CC1/2: 0.478 / Rpim(I) all: 0.835 / Rrim(I) all: 1.405

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Processing

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

6lu7


Resolution: 2.85→46.48 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.836 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.439
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2784 874 5.042 %
Rwork0.2041 16459 -
all0.208 --
obs-17333 98.343 %
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: 56.792 Å2
Baniso -1Baniso -2Baniso -3
1--3.432 Å2-0 Å20 Å2
2--7.202 Å20 Å2
3----3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 46 54 4805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134869
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174402
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.6396613
X-RAY DIFFRACTIONr_angle_other_deg1.1971.56910214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6985611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14123.154241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.25515777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.141522
X-RAY DIFFRACTIONr_chiral_restr0.0610.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021018
X-RAY DIFFRACTIONr_nbd_refined0.2020.2908
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24112
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22296
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.299
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.220
X-RAY DIFFRACTIONr_nbd_other0.2140.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.30.22
X-RAY DIFFRACTIONr_mcbond_it4.286.012441
X-RAY DIFFRACTIONr_mcbond_other4.2596.0092440
X-RAY DIFFRACTIONr_mcangle_it6.9239.0043050
X-RAY DIFFRACTIONr_mcangle_other6.9239.0063051
X-RAY DIFFRACTIONr_scbond_it3.9376.3472428
X-RAY DIFFRACTIONr_scbond_other3.9366.3492429
X-RAY DIFFRACTIONr_scangle_it6.4739.3633562
X-RAY DIFFRACTIONr_scangle_other6.4729.3653563
X-RAY DIFFRACTIONr_lrange_it9.99868.5565110
X-RAY DIFFRACTIONr_lrange_other9.99768.565110
X-RAY DIFFRACTIONr_ncsr_local_group_10.1320.058902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.422480.3631237X-RAY DIFFRACTION99.6124
2.924-3.0040.379640.3421153X-RAY DIFFRACTION99.5094
3.004-3.090.35620.3131146X-RAY DIFFRACTION99.4239
3.09-3.1850.327720.2891094X-RAY DIFFRACTION99.3186
3.185-3.2890.304600.2741070X-RAY DIFFRACTION99.0359
3.289-3.4040.367500.241045X-RAY DIFFRACTION98.8267
3.404-3.5310.304520.242974X-RAY DIFFRACTION96.7924
3.531-3.6750.343590.224940X-RAY DIFFRACTION97.2736
3.675-3.8370.248450.194954X-RAY DIFFRACTION99.2056
3.837-4.0230.269410.174898X-RAY DIFFRACTION98.7382
4.023-4.2390.234580.175847X-RAY DIFFRACTION99.2325
4.239-4.4940.224470.162798X-RAY DIFFRACTION98.715
4.494-4.8010.279370.119749X-RAY DIFFRACTION97.8829
4.801-5.1810.132340.118723X-RAY DIFFRACTION98.5677
5.181-5.6680.289350.163659X-RAY DIFFRACTION97.8843
5.668-6.3250.262200.19598X-RAY DIFFRACTION97.4763
6.325-7.2810.299200.142541X-RAY DIFFRACTION95.8974
7.281-8.8640.162210.131458X-RAY DIFFRACTION96.3783

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