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- PDB-7vk6: Crystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13 -

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Basic information

Entry
Database: PDB / ID: 7vk6
TitleCrystal Structure of SARS-CoV-2 Mpro at 2.25 A resolution-13
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 / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / 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 activation of host autophagy / viral translational frameshifting / cysteine-type endopeptidase activity / symbiont-mediated suppression of host gene expression / lipid binding / : / 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 / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Trypsin-like serine proteases / Macro domain / Macro domain profile. / Macro domain-like / Thrombin, subunit H / 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: 2.25 Å
AuthorsDeMirci, H. / Yuksel, B.
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
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-11 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.300, 105.500, 69.100
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.: 103 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
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: 2.2→41.93 Å / Num. obs: 39491 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 26.18 Å2 / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID% possible all
2.2-2.27133770.9931100
2.25-16.8116540.993199.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CWC

7cwc


Resolution: 2.25→16.82 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 833 2.27 %
Rwork0.2329 35935 -
obs0.2336 36768 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.07 Å2 / Biso mean: 60.3596 Å2 / Biso min: 25.97 Å2
Refinement stepCycle: final / Resolution: 2.25→16.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 0 103 4745
Biso mean---56.41 -
Num. residues----599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.390.3841390.367159026041
2.39-2.570.42341340.383759106044
2.57-2.830.33631340.302159196053
2.83-3.240.28071410.245759646105
3.24-4.070.22581380.201260376175
4.07-16.820.21471470.175162036350
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)
11.0298-1.11560.98413.1207-2.05392.2517-0.1842-0.18010.06180.15250.0095-0.04580.09780.19940.18020.3934-0.0372-0.00320.33910.01340.2974-8.1721-19.1218.193
20.714-1.0251.21569.7963-3.72332.0481-0.1901-0.20820.22240.98220.1473-0.5089-0.50860.01070.28710.6316-0.00470.01690.484-0.01470.373-3.2054-28.757734.3527
31.5314-0.84460.18653.0833-0.09994.6238-0.0713-0.27240.03120.6815-0.07870.0798-0.25930.0760.14810.3467-0.04620.04120.3225-0.03420.3461-12.5114-20.938221.3624
43.5720.9458-2.40985.16643.45326.41410.34890.02280.4362-0.2264-0.2474-0.2635-0.02720.2851-0.28810.42550.0284-0.00650.37180.01670.3756-5.848-23.66459.5888
50.18760.91780.4171.3550.14014.906-0.02050.4150.0022-0.19780.055-0.4330.66320.2233-0.13240.43290.05740.0450.3892-0.02820.3034-4.3932-32.947514.3359
64.8526-0.1377-2.28364.11451.36086.61160.1870.2884-0.06550.0782-0.08480.1044-0.1024-0.4608-0.12370.43020.0056-0.02130.4506-0.08080.2636-9.5579-37.0656-14.6922
79.42934.3688-5.2984.6692-3.0989.146-0.0812-0.62950.0687-0.2253-0.06810.0038-1.05660.02450.1710.5366-0.0553-0.13640.337-0.07920.2703-6.2782-26.0564-10.3991
81.79820.6172-0.85083.803-2.123.2254-0.1650.5312-0.1311-0.06730.13440.2564-0.0001-0.42180.02430.21270.0020.01490.34620.03950.3002-11.4295-0.6415-0.6725
95.8317-0.1345-2.57587.1542-2.55963.61830.14721.4040.7559-1.65330.2530.86250.3909-0.4929-0.07770.6510.0886-0.22850.99120.17980.6559-17.767810.3499-14.7702
101.8588-1.2344-1.38215.6018-0.1283.4646-0.04630.2057-0.0197-0.15880.09180.3850.0425-0.0790.10350.2072-0.0608-0.02440.3316-0.01510.3236-9.23534.45290.7199
116.1657-2.8298-5.12896.7265-0.02685.9884-0.54970.0553-0.27060.04320.36510.34720.1816-0.53470.02810.29170.0822-0.00510.36440.09190.3432-3.1029-7.2175-3.1076
123.5785-0.0846-0.98494.1448-0.34845.95910.25470.6966-0.2646-0.59620.03320.24370.56350.1252-0.22670.39320.08930.03770.3952-0.00730.2677-1.2986-1.4259-11.7368
139.1355-7.15550.98176.24771.06584.70480.0932-0.01021.199-0.3667-0.2019-1.4258-0.34740.24420.0440.39480.04690.08960.41190.08170.59222.3777-17.1892-3.8023
143.6887-4.2878-0.09534.87541.3853.334-0.4707-0.2161-1.69710.87010.23181.93040.6107-1.14060.08920.63110.07880.00450.6680.0410.966211.4551-20.1891-0.2318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A1 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 70 )A44 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 120 )A71 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 155 )A121 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 200 )A156 - 200
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 274 )A201 - 274
7X-RAY DIFFRACTION7chain 'A' and (resid 275 through 300 )A275 - 300
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 43 )B3 - 43
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 70 )B44 - 70
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 120 )B71 - 120
11X-RAY DIFFRACTION11chain 'B' and (resid 121 through 155 )B121 - 155
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 200 )B156 - 200
13X-RAY DIFFRACTION13chain 'B' and (resid 201 through 274 )B201 - 274
14X-RAY DIFFRACTION14chain 'B' and (resid 275 through 301 )B275 - 301

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