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- PDB-7vk5: Crystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-8 -

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Basic information

Entry
Database: PDB / ID: 7vk5
TitleCrystal Structure of SARS-CoV-2 Mpro at 2.10 A resolution-8
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / SFX
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
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsDeMirci, H. / Gocenler, O.
Funding support United States, Turkey, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
Other government118C270 Turkey
CitationJournal: Crystals / Year: 2021
Title: Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography
Authors: Guven, O. / Gul, M. / Ayan, E. / Johnson, J.A. / Cakilkaya, B. / Usta, G. / Ertem, F.B. / Tokay, N. / Yuksel, B. / Gocenler, O. / Buyukdag, C. / Botha, S. / Ketawala, G. / Su, Z. / Hayes, B. ...Authors: Guven, O. / Gul, M. / Ayan, E. / Johnson, J.A. / Cakilkaya, B. / Usta, G. / Ertem, F.B. / Tokay, N. / Yuksel, B. / Gocenler, O. / Buyukdag, C. / Botha, S. / Ketawala, G. / Su, Z. / Hayes, B. / Poitevin, F. / Batyuk, A. / Yoon, C.H. / Kupitz, C. / Durdagi, S. / Sierra, R.G. / DeMirci, H.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.200, 104.300, 105.600
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 / main protease


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 (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 294 K / Method: batch mode / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.25 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Aug 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.1→47.11 Å / Num. obs: 45382 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
2.1-2.16136650.9961100
2.1-47.1116910.996199.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CWC

7cwc


Resolution: 2.17→47.11 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1811 4.41 %
Rwork0.2407 39281 -
obs0.242 41092 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 57.4932 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: final / Resolution: 2.17→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 0 79 4721
Biso mean---52.7 -
Num. residues----599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.230.44951340.44042971310599
2.23-2.290.39441400.396329723112100
2.29-2.370.36811340.326929923126100
2.37-2.450.38091390.336529743113100
2.45-2.550.49791360.444329963132100
2.55-2.670.38471340.324329903124100
2.67-2.810.31421370.27230023139100
2.81-2.980.31991420.24930133155100
2.98-3.210.29321410.241730123153100
3.21-3.540.23281390.217830223161100
3.54-4.050.22751430.189230523195100
4.05-5.10.21071410.18630853226100
5.1-47.110.23881510.22883200335199
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)
12.68250.28961.39981.11450.93683.32920.0118-0.2919-0.05960.0757-0.05580.1392-0.0191-0.40580.05390.30950.03040.01180.32580.04380.3235-22.57968.5434-21.9913
25.93340.2627-0.60790.47080.59322.51280.00770.237-0.43060.0733-0.0652-0.07690.27520.04910.04390.30330.0316-0.01860.26790.03210.3312-8.83345.9134-30.1547
33.7747-0.15241.47372.1569-1.02945.36360.05350.07770.0922-0.11370.0483-0.06450.05950.26130.09820.40620.02690.10130.4385-0.01180.461218.07857.2878-39.5996
45.2018-0.1415-0.96673.1032-0.3952.18840.0267-0.39510.37980.25360.08130.157-0.14740.0626-0.12660.2849-0.00010.05360.4015-0.01640.384412.03569.0924-32.9726
52.6755-0.88071.2642.8613-0.13353.7961-0.1465-0.17320.47970.1638-0.0748-0.4325-0.57250.30670.14880.3163-0.0382-0.04370.26120.00750.37863.306311.63423.2689
62.0177-0.04431.38063.33182.60684.7264-0.20250.16550.0979-0.230.2793-0.1478-0.11710.4075-0.10710.2884-0.01520.01220.2944-0.01210.28267.5712-1.0779-5.3001
74.6530.0551-1.0383.52880.66972.9565-0.5423-0.3756-0.651.050.5824-0.57290.09870.4090.22460.78550.2285-0.18410.5355-0.14480.51696.1904-25.1735-19.8964
87.10210.00460.21917.33634.4515.7135-0.0391-0.22670.47910.47220.01660.0850.290.20970.01320.6806-0.03410.00010.3727-0.01690.39072.498-18.0465-17.1956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 129 )A2 - 129
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 213 )A130 - 213
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 236 )A214 - 236
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 300 )A237 - 300
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 129 )B3 - 129
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 213 )B130 - 213
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 236 )B214 - 236
8X-RAY DIFFRACTION8chain 'B' and (resid 237 through 300 )B237 - 300

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