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- PDB-8ddl: SARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure -

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Basic information

Entry
Database: PDB / ID: 8ddl
TitleSARS-CoV-2 Main Protease (Mpro) H163A Mutant Apo Structure
Components(ORF1a polyprotein) x 2
KeywordsHYDROLASE / cysteine protease / SARS-CoV-2 / 3CL-like / disulfide bond / VIRAL PROTEIN
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
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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / ORF1a polyprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTran, N. / McLeod, M.J. / Kalyaanamoorthy, S. / Ganesan, A. / Holyoak, T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Nat Commun / Year: 2023
Title: The H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease.
Authors: Tran, N. / Dasari, S. / Barwell, S.A.E. / McLeod, M.J. / Kalyaanamoorthy, S. / Holyoak, T. / Ganesan, A.
History
DepositionJun 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF1a polyprotein
B: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1318
Polymers67,5332
Non-polymers5986
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-13 kcal/mol
Surface area26300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.832, 101.463, 102.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ORF1a polyprotein


Mass: 33758.477 Da / Num. of mol.: 1 / Mutation: H163A
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: A0A7U3EDN3
#2: Protein ORF1a polyprotein


Mass: 33774.477 Da / Num. of mol.: 1 / Mutation: H163A
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: A0A7U3EDN3

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Non-polymers , 5 types, 382 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.61 Å3/Da / Density % sol: 52.81 % / Description: Thin plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5 and 26% (v/v) PEG Smear Broad (BCS B11)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.95→102.95 Å / Num. obs: 52678 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.047 / Rrim(I) all: 0.176 / Net I/σ(I): 6.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 14.04 % / Rmerge(I) obs: 1.082 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2569 / CC1/2: 0.759 / Rpim(I) all: 0.297 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS3.8.0data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ALH

7alh


Resolution: 1.95→56.54 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 19.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2661 5.06 %
Rwork0.1683 --
obs0.1702 52592 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→56.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 39 376 5047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054884
X-RAY DIFFRACTIONf_angle_d0.7586655
X-RAY DIFFRACTIONf_dihedral_angle_d13.6481797
X-RAY DIFFRACTIONf_chiral_restr0.05753
X-RAY DIFFRACTIONf_plane_restr0.005867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.28211310.23092354X-RAY DIFFRACTION91
1.98-2.010.25821260.21132616X-RAY DIFFRACTION100
2.01-2.060.1941130.19652622X-RAY DIFFRACTION100
2.06-2.10.24641540.18022583X-RAY DIFFRACTION100
2.1-2.150.24311350.17312630X-RAY DIFFRACTION100
2.15-2.20.2161130.17232624X-RAY DIFFRACTION100
2.2-2.260.2321490.17292623X-RAY DIFFRACTION100
2.26-2.330.22591300.1752629X-RAY DIFFRACTION100
2.33-2.40.21561280.18012608X-RAY DIFFRACTION100
2.4-2.490.24581890.19022578X-RAY DIFFRACTION100
2.49-2.590.21671440.1832608X-RAY DIFFRACTION100
2.59-2.710.25721610.18562633X-RAY DIFFRACTION100
2.71-2.850.23821200.18112644X-RAY DIFFRACTION100
2.85-3.030.20691260.18152654X-RAY DIFFRACTION100
3.03-3.260.25841530.19282642X-RAY DIFFRACTION100
3.26-3.590.19831450.16352665X-RAY DIFFRACTION100
3.59-4.110.17271280.1472692X-RAY DIFFRACTION100
4.11-5.180.1511550.13292705X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9932-1.6172-0.10353.26350.9162.8555-0.2057-0.44360.29160.4890.17080.0484-0.1397-0.21570.02520.28570.03110.00470.2202-0.03910.183212.987432.0259-11.0949
23.7793-0.42620.82972.52010.9141.7130.0226-0.1394-0.11640.1802-0.03550.22760.0862-0.14650.0080.18890.00980.02030.1604-0.01650.151210.344821.8663-23.4512
34.2923-0.6186-0.65315.06072.39966.194-0.06510.0324-0.0452-0.2007-0.05760.1874-0.286-0.08830.10690.25910.0349-0.00840.1769-0.02590.160813.90148.3233-44.8073
43.9707-1.869-0.45582.04290.28661.07680.06390.1289-0.0322-0.1897-0.0245-0.1377-0.02030.0318-0.0550.2036-0.02890.01240.13860.01190.153936.81925.6991-19.3667
53.5155-2.9193-0.82575.91821.95262.264-0.0938-0.14140.5569-0.07110.2212-0.6942-0.16040.3639-0.12740.1764-0.05070.02990.2619-0.02130.332151.1883.5365-18.6427
63.07641.26310.15763.51710.78231.2501-0.0487-0.3249-0.06780.19630.1052-0.2593-0.06040.0581-0.07270.19730.0317-0.03840.21630.01240.157738.48943.0677-9.607
73.14752.21461.30666.43691.18830.9623-0.17710.5042-0.0596-0.99040.198-0.4098-0.20760.14520.02520.30420.01280.04510.23540.01240.235526.39982.9415-23.2549
85.2117-0.7861-0.48222.30220.3021.25790.03590.1658-0.3172-0.08540.0639-0.05050.0167-0.0433-0.11470.1502-0.0171-0.00560.1310.02980.176930.2731-3.4582-19.546
93.33490.72640.62374.55610.423.1096-0.0092-0.1712-0.05620.05670.05190.13440.062-0.2157-0.04090.1475-0.0296-0.00420.23540.03220.19672.4869-8.8739-16.9025
102.65010.72723.516.1858-2.7137.1132-0.2015-0.20650.67280.40810.02460.1881-0.8638-0.87320.06040.2043-0.0027-0.00130.322-0.00640.358810.19821.0664-13.6282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 301 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 50 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 110 )
7X-RAY DIFFRACTION7chain 'B' and (resid 111 through 143 )
8X-RAY DIFFRACTION8chain 'B' and (resid 144 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 284 )
10X-RAY DIFFRACTION10chain 'B' and (resid 285 through 302 )

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