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- PDB-7ntv: Crystal structure of SARS CoV2 main protease in complex with DN_E... -

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Basic information

Entry
Database: PDB / ID: 7ntv
TitleCrystal structure of SARS CoV2 main protease in complex with DN_EG_002 (modelled using PanDDA event map)
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 / methylation / double membrane vesicle viral factory outer membrane ...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 / methylation / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / cysteine-type endopeptidase activity / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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. / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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-US8 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.065 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 10, 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)68,49810
Polymers67,6512
Non-polymers8478
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint1 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.941, 99.743, 104.126
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
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-US8 / 2-acetamido-N-cyclopropyl-5-phenyl-thiophene-3-carboxamide / 2-acetamido-~{N}-cyclopropyl-5-phenyl-thiophene-3-carboxamide


Mass: 300.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
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 DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 by adding the stock to ...Details: 0.1 M MES pH 6.5 15% w/v PEG 6000 5% v/v MPD Compound stock DN_EG_002 100 mM in 100% DMSO Crystals were soaked for 3 hours with final concentration of 10 mM DN_EG_002 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: 1.00003 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: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.065→49.423 Å / Num. obs: 44110 / % possible obs: 99.82 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.044 / Rrim(I) all: 0.164 / Net I/σ(I): 11
Reflection shellResolution: 2.065→2.119 Å / Redundancy: 13.75 % / Rmerge(I) obs: 1.961 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3361 / CC1/2: 0.71 / Rpim(I) all: 0.54 / % possible all: 98.9

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Processing

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

6lu7


Resolution: 2.065→49.423 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.568 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.164
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2203 5.001 %RANDOM
Rwork0.1949 41846 --
all0.196 ---
obs-44049 99.814 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 42.474 Å2
Baniso -1Baniso -2Baniso -3
1--1.753 Å20 Å2-0 Å2
2--2.332 Å20 Å2
3----0.579 Å2
Refinement stepCycle: LAST / Resolution: 2.065→49.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 49 122 4858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174420
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.646699
X-RAY DIFFRACTIONr_angle_other_deg1.3691.56810258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5825618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88723.036247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11615776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2261522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
X-RAY DIFFRACTIONr_nbd_refined0.20.2893
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.24157
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22389
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2240.221
X-RAY DIFFRACTIONr_nbd_other0.2560.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.24
X-RAY DIFFRACTIONr_mcbond_it3.544.2862500
X-RAY DIFFRACTIONr_mcbond_other3.5434.2832492
X-RAY DIFFRACTIONr_mcangle_it5.076.423080
X-RAY DIFFRACTIONr_mcangle_other5.076.4223081
X-RAY DIFFRACTIONr_scbond_it4.574.8592519
X-RAY DIFFRACTIONr_scbond_other4.5694.862520
X-RAY DIFFRACTIONr_scangle_it6.9117.0263613
X-RAY DIFFRACTIONr_scangle_other6.917.0283614
X-RAY DIFFRACTIONr_lrange_it8.67250.1795222
X-RAY DIFFRACTIONr_lrange_other8.66850.1435212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.065-2.1190.3431600.3283037X-RAY DIFFRACTION98.8865
2.119-2.1770.3091560.2872957X-RAY DIFFRACTION99.9679
2.177-2.240.2651510.2642866X-RAY DIFFRACTION99.9669
2.24-2.3090.3011490.252841X-RAY DIFFRACTION100
2.309-2.3840.281430.2422722X-RAY DIFFRACTION99.9302
2.384-2.4680.2941380.2372629X-RAY DIFFRACTION99.9639
2.468-2.5610.2751350.2312562X-RAY DIFFRACTION99.7043
2.561-2.6650.2791290.2232451X-RAY DIFFRACTION99.9613
2.665-2.7830.2861240.2112364X-RAY DIFFRACTION99.8395
2.783-2.9180.2011200.1962277X-RAY DIFFRACTION100
2.918-3.0760.2541130.1942163X-RAY DIFFRACTION100
3.076-3.2610.2431090.1992062X-RAY DIFFRACTION100
3.261-3.4850.2371020.1881923X-RAY DIFFRACTION100
3.485-3.7630.211950.1861805X-RAY DIFFRACTION99.4244
3.763-4.120.179870.1641664X-RAY DIFFRACTION100
4.12-4.6020.174810.141528X-RAY DIFFRACTION100
4.602-5.3060.16720.1431356X-RAY DIFFRACTION100
5.306-6.480.232610.2041159X-RAY DIFFRACTION100
6.48-9.0870.185480.164914X-RAY DIFFRACTION98.768

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