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Entry
Database: PDB / ID: 7cwb
TitleAmbient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 1.9 A Resolution (C121)
Components3C-like proteinase
KeywordsVIRAL PROTEIN / COVID19 / SARS-CoV-2 / Drug Target / Serial Femtosecond X-ray Crystallography / SFX / XFEL / Virus Protein
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core 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 / 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. / : / :
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsDeMirci, H.
Funding support United States, Turkey, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
National Science Foundation (NSF, United States)118C260 Turkey
CitationJournal: Structure / Year: 2021
Title: Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.
Authors: Durdagi, S. / Dag, C. / Dogan, B. / Yigin, M. / Avsar, T. / Buyukdag, C. / Erol, I. / Ertem, F.B. / Calis, S. / Yildirim, G. / Orhan, M.D. / Guven, O. / Aksoydan, B. / Destan, E. / Sahin, K. ...Authors: Durdagi, S. / Dag, C. / Dogan, B. / Yigin, M. / Avsar, T. / Buyukdag, C. / Erol, I. / Ertem, F.B. / Calis, S. / Yildirim, G. / Orhan, M.D. / Guven, O. / Aksoydan, B. / Destan, E. / Sahin, K. / Besler, S.O. / Oktay, L. / Shafiei, A. / Tolu, I. / Ayan, E. / Yuksel, B. / Peksen, A.B. / Gocenler, O. / Yucel, A.D. / Can, O. / Ozabrahamyan, S. / Olkan, A. / Erdemoglu, E. / Aksit, F. / Tanisali, G. / Yefanov, O.M. / Barty, A. / Tolstikova, A. / Ketawala, G.K. / Botha, S. / Dao, E.H. / Hayes, B. / Liang, M. / Seaberg, M.H. / Hunter, M.S. / Batyuk, A. / Mariani, V. / Su, Z. / Poitevin, F. / Yoon, C.H. / Kupitz, C. / Sierra, R.G. / Snell, E.H. / DeMirci, H.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Structure summary / Category: entity_name_com / Item: _entity_name_com.name
Revision 1.2May 19, 2021Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.3Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)33,8261
Polymers33,8261
Non-polymers00
Water1,982110
1
A: 3C-like proteinase

A: 3C-like proteinase


Theoretical massNumber of molelcules
Total (without water)67,6512
Polymers67,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3190 Å2
ΔGint-17 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.000, 53.500, 45.000
Angle α, β, γ (deg.)90.000, 102.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

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Components

#1: Protein 3C-like proteinase / main protease / 3CL-PRO / 3CLp / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 294 K / Method: batch mode / Details: 0.1 M MMT 6.0, 25% w/v PEG 1500

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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: 1.29 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.29 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 26291 / % possible obs: 99.91 % / Redundancy: 825 % / CC1/2: 0.996 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→1.98 Å / Num. unique obs: 2650 / CC1/2: 0.79

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å34.08 Å

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Processing

Software
NameVersionClassification
PHASER2.8.3phasing
PHENIXphenix-dev-3318refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wqf

6wqf


Resolution: 1.9→34.076 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1997 9.5 %
Rwork0.2181 19032 -
obs0.2218 21029 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.04 Å2 / Biso mean: 42.9958 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 1.9→34.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 113 2480
Biso mean---51.38 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94750.49191430.43081359100
1.9475-2.00020.42491420.39121352100
2.0002-2.0590.3871420.34561357100
2.059-2.12550.31341380.26881328100
2.1255-2.20140.28471420.24471346100
2.2014-2.28960.28451420.24321351100
2.2896-2.39370.30481420.24371356100
2.3937-2.51990.27331440.23841369100
2.5199-2.67770.30621410.23011347100
2.6777-2.88440.27151430.21321354100
2.8844-3.17440.23841440.20541374100
3.1744-3.63330.20511420.17981356100
3.6333-4.57590.21831440.17421379100
4.5759-340.23851480.2204140499
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)
13.973-0.07522.51021.49161.02413.09710.677-0.5393-0.57780.333-0.0746-0.06571.2685-0.2442-0.26250.5029-0.0748-0.05210.29360.09390.329611.3575-20.719816.3856
23.8490.5341.71823.59290.11543.36690.162-0.0842-0.0572-0.1037-0.1212-0.01510.18140.2036-0.02320.16540.01010.02310.16660.02390.180511.2834-9.81537.6314
31.8326-0.09230.9351.2888-1.07885.7034-0.11120.44530.2758-0.0985-0.02760.0173-0.57290.3806-0.00270.2305-0.08330.01460.25440.07120.285613.27856.3853-6.7007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 100 )A1 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 180 )A101 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 306 )A181 - 306

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