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- PDB-9gi6: Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A -

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Basic information

Entry
Database: PDB / ID: 9gi6
TitleStructure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A
ComponentsReplicase polyprotein 1a
KeywordsHYDROLASE / SARS-CoV-2 / main protease / mutation / N214A
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / 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 ...host cell membrane / viral genome replication / methyltransferase activity / 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 / cysteine-type deubiquitinase activity / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / 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 / 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
DI(HYDROXYETHYL)ETHER / ORF1a polyprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCreon, A. / Scheer, T.E.S. / Lane, T.J. / Rahmani Mashhour, A. / Guenther, S. / Reinke, P.Y.A. / Meents, A. / Chapman, H.N.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of SARS-CoV-2 Main Protease (Mpro) with mutation of N214A
Authors: Creon, A. / Scheer, T.E.S. / Lane, T.J. / Rahmani Mashhour, A. / Guenther, S. / Reinke, P.Y.A. / Meents, A. / Chapman, H.N.
History
DepositionAug 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,08728
Polymers67,5652
Non-polymers2,52226
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint37 kcal/mol
Surface area24930 Å2
Unit cell
Length a, b, c (Å)67.807, 100.574, 102.182
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

#1: Protein Replicase polyprotein 1a / ORF1a polyprotein


Mass: 33782.523 Da / Num. of mol.: 2 / Mutation: N214A
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: A0A6M4EPN9
#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 52.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.12 M ethylene glycols (Diethylene glycol; Triethylene glycol; Tetraethylene glycol; Pentaethylene glycol); 0.1 M buffer system 3 (Morpheus; 1.0 M Tris (base), BICINE); pH 8.5 and 50% (v/v) ...Details: 0.12 M ethylene glycols (Diethylene glycol; Triethylene glycol; Tetraethylene glycol; Pentaethylene glycol); 0.1 M buffer system 3 (Morpheus; 1.0 M Tris (base), BICINE); pH 8.5 and 50% (v/v) Precipitant Mix 1 (Morpheus; 40 % (v/v) PEG 500 MME, 20 % (w/v) PEG 20000)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0322 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0322 Å / Relative weight: 1
ReflectionResolution: 1.83→55.28 Å / Num. obs: 42912 / % possible obs: 94.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 60.38 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.1
Reflection shellResolution: 1.83→2.01 Å / Num. unique obs: 15980 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→55.28 Å / SU ML: 0.1801 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 2011 4.69 %
Rwork0.1739 40893 -
obs0.1756 42904 68.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.26 Å2
Refinement stepCycle: LAST / Resolution: 1.83→55.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 164 310 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725012
X-RAY DIFFRACTIONf_angle_d0.85426761
X-RAY DIFFRACTIONf_chiral_restr0.0522747
X-RAY DIFFRACTIONf_plane_restr0.0066872
X-RAY DIFFRACTIONf_dihedral_angle_d14.60551819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.880.244370.1833124X-RAY DIFFRACTION3.01
1.88-1.930.2498230.2332417X-RAY DIFFRACTION10.03
1.93-1.980.2712360.2204877X-RAY DIFFRACTION20.81
1.98-2.050.236890.22321718X-RAY DIFFRACTION40.92
2.05-2.120.23721170.20662373X-RAY DIFFRACTION56.41
2.12-2.210.22961440.18712811X-RAY DIFFRACTION67.28
2.21-2.310.23051610.19563275X-RAY DIFFRACTION77.95
2.31-2.430.23311840.19073651X-RAY DIFFRACTION86.55
2.43-2.580.24821980.18864118X-RAY DIFFRACTION97.6
2.58-2.780.21692000.18594233X-RAY DIFFRACTION99.71
2.78-3.060.2062120.18094248X-RAY DIFFRACTION99.96
3.06-3.50.2282100.17214289X-RAY DIFFRACTION100
3.5-4.410.1762070.15124312X-RAY DIFFRACTION99.85
4.41-55.280.18132230.1584447X-RAY DIFFRACTION98.79
Refinement TLS params.Method: refined / Origin x: -2.67979885065 Å / Origin y: -2.98368345403 Å / Origin z: 16.4820626626 Å
111213212223313233
T0.0578315575939 Å20.0109675552638 Å2-0.00269514203662 Å2-0.22568708769 Å2-0.0190263776798 Å2--0.10381805125 Å2
L0.787496038306 °20.0848586274182 °2-0.0821722594998 °2-0.472546608848 °2-0.196338561272 °2--1.47672507904 °2
S0.026403174117 Å °-0.0221608488744 Å °-0.013869204132 Å °-0.04106979739 Å °-0.0344233593201 Å °-0.0658395695512 Å °-0.00360792309633 Å °0.0773532180979 Å °0.00220917838663 Å °
Refinement TLS groupSelection details: all

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