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- PDB-9ez6: Complex of a mutant of the SARS-CoV-2 main protease Mpro with the... -

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Basic information

Entry
Database: PDB / ID: 9ez6
TitleComplex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.
Components
  • Replicase polyprotein 1a
  • THR-PHE-THR-ARG-LEU-GLN-SER-LEU-GLU-ASN
KeywordsHYDROLASE / SARS-CoV-2 / main protease / nsp5 / Cys-peptidase / 3CLpro
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity ...viral genome replication / methyltransferase activity / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / 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 / 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 / Betacoronavirus Nsp3c-M domain profile. ...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 / 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
GLUTAMINE / DI(HYDROXYETHYL)ETHER / ORF1a polyprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBattistutta, R. / Fornasier, E. / Giachin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: Allostery in homodimeric SARS-CoV-2 main protease.
Authors: Fornasier, E. / Fabbian, S. / Shehi, H. / Enderle, J. / Gatto, B. / Volpin, D. / Biondi, B. / Bellanda, M. / Giachin, G. / Sosic, A. / Battistutta, R.
History
DepositionApr 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1a
B: Replicase polyprotein 1a
C: THR-PHE-THR-ARG-LEU-GLN-SER-LEU-GLU-ASN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,17322
Polymers68,8673
Non-polymers1,30519
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint11 kcal/mol
Surface area24190 Å2
Unit cell
Length a, b, c (Å)67.802, 99.032, 100.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein Replicase polyprotein 1a / ORF1a polyprotein


Mass: 33758.410 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 (E. coli) / References: UniProt: A0A8B1KJN1
#2: Protein/peptide THR-PHE-THR-ARG-LEU-GLN-SER-LEU-GLU-ASN


Mass: 1350.497 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 6 types, 204 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MMT (DL-malic acid, MES, and Tris base in molar ratio 1:2:2), pH 7.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.87→55.95 Å / Num. obs: 55875 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 37.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Rsym value: 0.057 / Net I/σ(I): 10.5
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3408 / CC1/2: 0.536 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Rsym value: 0.057

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→55.95 Å / SU ML: 0.2639 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 2742 4.91 %
Rwork0.1946 53068 -
obs0.1962 55810 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.18 Å2
Refinement stepCycle: LAST / Resolution: 1.87→55.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 84 185 4991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724916
X-RAY DIFFRACTIONf_angle_d0.73156647
X-RAY DIFFRACTIONf_chiral_restr0.0478746
X-RAY DIFFRACTIONf_plane_restr0.0062859
X-RAY DIFFRACTIONf_dihedral_angle_d14.25681756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.42061370.38372518X-RAY DIFFRACTION94.72
1.9-1.940.33561600.30522533X-RAY DIFFRACTION95.5
1.94-1.970.30151470.26172561X-RAY DIFFRACTION98.04
1.97-2.010.29291220.23812629X-RAY DIFFRACTION98.18
2.01-2.060.24241500.22752606X-RAY DIFFRACTION98.08
2.06-2.110.24241210.21592669X-RAY DIFFRACTION99.29
2.11-2.160.2481280.22112628X-RAY DIFFRACTION98.89
2.16-2.220.26721300.23132659X-RAY DIFFRACTION98.38
2.22-2.280.27011260.22192647X-RAY DIFFRACTION98.58
2.28-2.360.23121090.20062654X-RAY DIFFRACTION97.87
2.36-2.440.24021190.19042668X-RAY DIFFRACTION99.15
2.44-2.540.23411570.18242648X-RAY DIFFRACTION99.26
2.54-2.650.22751200.18792702X-RAY DIFFRACTION99.33
2.65-2.790.2541590.19042669X-RAY DIFFRACTION99.54
2.79-2.970.2661470.21182678X-RAY DIFFRACTION99.16
2.97-3.20.22131390.19132685X-RAY DIFFRACTION99.16
3.2-3.520.19821520.18072661X-RAY DIFFRACTION98.29
3.52-4.030.2081110.17232737X-RAY DIFFRACTION98.34
4.03-5.070.18351570.15632685X-RAY DIFFRACTION97.66
5.08-55.950.23971510.21752831X-RAY DIFFRACTION97.58
Refinement TLS params.Method: refined / Origin x: 3.2403210253 Å / Origin y: -2.69417360541 Å / Origin z: -16.7704942892 Å
111213212223313233
T0.23566108077 Å2-0.0164022054046 Å20.000782986145967 Å2-0.221425423314 Å20.0286902240366 Å2--0.270038854215 Å2
L0.931390493234 °20.0546291123138 °20.0504588681556 °2-0.585212111832 °20.117417431392 °2--2.45038467377 °2
S0.0631391947389 Å °-0.0974385568188 Å °0.0186420347929 Å °0.0677083452441 Å °-0.00995540696363 Å °0.0214773254662 Å °0.0016793999824 Å °-0.277811217447 Å °-0.0496443343568 Å °
Refinement TLS groupSelection details: all

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