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- PDB-7tix: Crystal structure of SARS-CoV-2 3CL in complex with inhibitor EB56 -

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Basic information

Entry
Database: PDB / ID: 7tix
TitleCrystal structure of SARS-CoV-2 3CL in complex with inhibitor EB56
Components3C-like proteinase nsp5
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR complex
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 / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / viral translational frameshifting / symbiont-mediated activation of host autophagy / 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 / 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 / : / : / 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 / Trypsin-like serine proteases / Appr-1"-p processing enzyme / Macro domain / 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
Chem-Q56 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsForouhar, F. / Liu, H. / Iketani, S. / Zack, A. / Khanizeman, N. / Bednarova, E. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. ...Forouhar, F. / Liu, H. / Iketani, S. / Zack, A. / Khanizeman, N. / Bednarova, E. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, S.J. / Quinn, C. / Li, W. / Shion, H. / Jurtschenko, C. / Lauber, M.A. / McDonald, T. / Stokes, M.E. / Hurst, B. / Rovis, T. / Chavez, A. / Ho, D.D. / Stockwell, B.R.
Funding support7items
OrganizationGrant numberCountry
Jack Ma Foundation
Burroughs Wellcome Fund
Columbia Technology Ventures
Columbia Translational Therapeutics (TRx)
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI106711
National Science Foundation (NSF, United States)2029943
Department of Energy (DOE, United States)DE-AC02-06CH11357
CitationJournal: Nat Commun / Year: 2022
Title: Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.
Authors: Liu, H. / Iketani, S. / Zask, A. / Khanizeman, N. / Bednarova, E. / Forouhar, F. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, ...Authors: Liu, H. / Iketani, S. / Zask, A. / Khanizeman, N. / Bednarova, E. / Forouhar, F. / Fowler, B. / Hong, S.J. / Mohri, H. / Nair, M.S. / Huang, Y. / Tay, N.E.S. / Lee, S. / Karan, C. / Resnick, S.J. / Quinn, C. / Li, W. / Shion, H. / Xia, X. / Daniels, J.D. / Bartolo-Cruz, M. / Farina, M. / Rajbhandari, P. / Jurtschenko, C. / Lauber, M.A. / McDonald, T. / Stokes, M.E. / Hurst, B.L. / Rovis, T. / Chavez, A. / Ho, D.D. / Stockwell, B.R.
History
DepositionJan 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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

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Assembly

Deposited unit
A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3853
Polymers33,8261
Non-polymers5602
Water2,432135
1
A: 3C-like proteinase nsp5
hetero molecules

A: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7716
Polymers67,6512
Non-polymers1,1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2680 Å2
ΔGint-6 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.729, 81.462, 54.566
Angle α, β, γ (deg.)90.000, 116.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-603-

HOH

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Components

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / 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
Production host: Escherichia coli (E. coli)
References: UniProt: P0DTC1, SARS coronavirus main proteinase
#2: Chemical ChemComp-Q56 / N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide


Mass: 535.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33N3O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.84 Å3/Da / Density % sol: 56.7 % / Description: block-shaped
Crystal growTemperature: 277 K / Method: microbatch / pH: 5
Details: 0.1 M potassium thiocyanate, 0.1 M sodium acetate, pH 5, and 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→59.3 Å / Num. obs: 28601 / % possible obs: 98.1 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Net I/σ(I): 10.6
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.329 / Mean I/σ(I) obs: 1 / Num. unique obs: 1573 / CC1/2: 0.61 / % possible all: 80.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JSU

7jsu


Resolution: 2→45.07 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 2557 10.06 %
Rwork0.1722 22871 -
obs0.1763 25428 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.82 Å2 / Biso mean: 49.0704 Å2 / Biso min: 21.38 Å2
Refinement stepCycle: final / Resolution: 2→45.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 34 138 2505
Biso mean--43.47 49.95 -
Num. residues----302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.040.33851340.276412581392100
2.04-2.080.32521490.255312511400100
2.08-2.130.30321560.24281250140699
2.13-2.170.25891310.218713051436100
2.17-2.230.24911500.20391229137999
2.23-2.290.24961340.20891278141299
2.29-2.360.29641300.21051296142699
2.36-2.430.24451660.19451251141799
2.43-2.520.23341640.18921224138898
2.52-2.620.19981320.188812691401100
2.62-2.740.24721600.186212631423100
2.74-2.880.24511430.185112701413100
2.88-3.060.23271440.19281273141799
3.07-3.30.221250.19281276140199
3.3-3.630.23891250.17351278140398
3.63-4.160.18231540.146212711425100
4.16-5.240.15661280.124913101438100
5.24-45.070.16471320.14411319145199
Refinement TLS params.Method: refined / Origin x: -5.4775 Å / Origin y: -1.1375 Å / Origin z: 12.1278 Å
111213212223313233
T0.237 Å2-0.0135 Å2-0.0127 Å2-0.254 Å2-0.0216 Å2--0.281 Å2
L0.7293 °20.3517 °2-0.505 °2-0.8772 °20.4544 °2--2.2554 °2
S0.0527 Å °-0.0663 Å °-0.0509 Å °0.0437 Å °0.0005 Å °-0.0739 Å °-0.1344 Å °-0.0681 Å °0.0176 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 302
2X-RAY DIFFRACTION1allA401 - 402
3X-RAY DIFFRACTION1allS1 - 138

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