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- PDB-7nt3: Crystal structure of SARS CoV2 main protease in complex with FSCU015 -

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Basic information

Entry
Database: PDB / ID: 7nt3
TitleCrystal structure of SARS CoV2 main protease in complex with FSCU015
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Protease / Complex
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 / endonuclease 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 / Trypsin-like serine proteases / 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 / Thrombin, subunit H / 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-UQZ / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.325 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)68,3607
Polymers67,6512
Non-polymers7095
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-6 kcal/mol
Surface area25390 Å2
Unit cell
Length a, b, c (Å)68.005, 101.348, 103.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
Gene: ORF1ab / 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-UQZ / ~{N}-[(1~{S})-2-(1,3-benzodioxol-5-ylmethylamino)-1-(3-hydroxyphenyl)-2-oxidanylidene-ethyl]-~{N}-propyl-prop-2-enamide


Mass: 396.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.65066648 Å3/Da / Density % sol: 53.6254044 %
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 FSCU015 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 FSCU015 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: 1.000031 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000031 Å / Relative weight: 1
ReflectionResolution: 2.32→49.62 Å / Num. obs: 31612 / % possible obs: 99.8 % / Redundancy: 9.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.081 / Rrim(I) all: 0.184 / Net I/σ(I): 9.3
Reflection shellResolution: 2.32→2.41 Å / Redundancy: 9.6 % / Rmerge(I) obs: 1.748 / Num. unique obs: 3014 / CC1/2: 0.606 / Rpim(I) all: 0.866 / Rrim(I) all: 1.956

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Processing

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

6lu7


Resolution: 2.325→46.302 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.231 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.259
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1626 5.153 %RANDOM
Rwork0.2063 29930 --
all0.21 ---
obs-31556 99.769 %-
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: 49.324 Å2
Baniso -1Baniso -2Baniso -3
1--3.228 Å2-0 Å20 Å2
2--6.182 Å2-0 Å2
3----2.954 Å2
Refinement stepCycle: LAST / Resolution: 2.325→46.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 45 126 4862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134849
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174365
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6396587
X-RAY DIFFRACTIONr_angle_other_deg1.251.56810128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73123.045243
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.51101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36215771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1271522
X-RAY DIFFRACTIONr_chiral_restr0.0620.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025479
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021019
X-RAY DIFFRACTIONr_nbd_refined0.1910.2884
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24181
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22339
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2151
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.219
X-RAY DIFFRACTIONr_nbd_other0.2590.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.27
X-RAY DIFFRACTIONr_mcbond_it3.5785.152431
X-RAY DIFFRACTIONr_mcbond_other3.5665.1472429
X-RAY DIFFRACTIONr_mcangle_it5.7217.713037
X-RAY DIFFRACTIONr_mcangle_other5.7127.7113037
X-RAY DIFFRACTIONr_scbond_it3.7745.5642418
X-RAY DIFFRACTIONr_scbond_other3.7735.5662419
X-RAY DIFFRACTIONr_scangle_it6.0998.1643550
X-RAY DIFFRACTIONr_scangle_other6.0988.1663551
X-RAY DIFFRACTIONr_lrange_it9.08459.2495157
X-RAY DIFFRACTIONr_lrange_other9.08859.2495150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.325-2.3850.3321220.3542136X-RAY DIFFRACTION98.1312
2.385-2.4510.4031200.3382128X-RAY DIFFRACTION100
2.451-2.5210.291200.3122063X-RAY DIFFRACTION100
2.521-2.5990.3631070.2822016X-RAY DIFFRACTION100
2.599-2.6840.3161120.2841937X-RAY DIFFRACTION100
2.684-2.7780.323970.2661896X-RAY DIFFRACTION100
2.778-2.8830.299960.2451844X-RAY DIFFRACTION99.9485
2.883-30.346820.2391755X-RAY DIFFRACTION100
3-3.1340.2781060.1991679X-RAY DIFFRACTION100
3.134-3.2860.282960.21612X-RAY DIFFRACTION99.4179
3.286-3.4640.217640.1831573X-RAY DIFFRACTION100
3.464-3.6730.281910.1971445X-RAY DIFFRACTION100
3.673-3.9260.267740.1831385X-RAY DIFFRACTION100
3.926-4.240.221760.1671300X-RAY DIFFRACTION100
4.24-4.6430.223610.1421193X-RAY DIFFRACTION100
4.643-5.1880.249570.1511101X-RAY DIFFRACTION100
5.188-5.9860.294430.184967X-RAY DIFFRACTION100
5.986-7.3180.27310.185853X-RAY DIFFRACTION99.4376
7.318-10.2970.185370.128660X-RAY DIFFRACTION100

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