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- PDB-7jit: The crystal structure of Papain-Like Protease of SARS CoV-2 , C11... -

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Basic information

Entry
Database: PDB / ID: 7jit
TitleThe crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, in complex with PLP_Snyder495 inhibitor
ComponentsPapain-like protease
KeywordsHYDROLASE/HYDROLASE inhibitor / covid-19 / coronavirus / SARS / CoV-2 / papain-like protease / IDP51000 / Center for Structural Genomics of Infectious Diseases / CSGID / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins ...viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 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 / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / methylation / 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 / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
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 / : ...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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / 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.
Similarity search - Domain/homology
ACETATE ION / Chem-Y95 / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOsipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. ...Osipiuk, J. / Tesar, C. / Endres, M. / Lisnyak, V. / Maki, S. / Taylor, C. / Zhang, Y. / Zhou, Z. / Azizi, S.A. / Jones, K. / Kathayat, R. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat Commun / Year: 2021
Title: Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors.
Authors: Osipiuk, J. / Azizi, S.A. / Dvorkin, S. / Endres, M. / Jedrzejczak, R. / Jones, K.A. / Kang, S. / Kathayat, R.S. / Kim, Y. / Lisnyak, V.G. / Maki, S.L. / Nicolaescu, V. / Taylor, C.A. / ...Authors: Osipiuk, J. / Azizi, S.A. / Dvorkin, S. / Endres, M. / Jedrzejczak, R. / Jones, K.A. / Kang, S. / Kathayat, R.S. / Kim, Y. / Lisnyak, V.G. / Maki, S.L. / Nicolaescu, V. / Taylor, C.A. / Tesar, C. / Zhang, Y.A. / Zhou, Z. / Randall, G. / Michalska, K. / Snyder, S.A. / Dickinson, B.C. / Joachimiak, A.
History
DepositionJul 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_description / _entity.pdbx_ec
Revision 1.2Feb 10, 2021Group: Database references / Category: 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
Revision 1.3Mar 31, 2021Group: Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / struct / struct_keywords
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Papain-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,99912
Polymers35,9281
Non-polymers1,07211
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.913, 113.913, 219.328
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Papain-like protease / Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 35927.695 Da / Num. of mol.: 1 / Mutation: C111S
Source method: isolated from a genetically manipulated source
Details: 3 N-terminal residues (SNA) are from expression tag
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTC1, UniProt: P0DTD1*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 6 types, 241 molecules

#2: Chemical ChemComp-Y95 / 5-[(carbamoylcarbamoyl)amino]-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide


Mass: 390.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.95 Å3/Da / Density % sol: 76.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES buffer, 0.2 M zinc acetate, 10% PEG 8000, 4 mM PLP_Snyder495

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→49.67 Å / Num. obs: 52219 / % possible obs: 99.5 % / Redundancy: 16.6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.024 / Rrim(I) all: 0.1 / Χ2: 1.218 / Net I/av σ(I): 35.2 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.989.51.2291.0823680.5590.3911.2960.98291.6
1.98-2.0212.11.29425580.6770.3811.3520.96798.6
2.02-2.0614.51.21325820.8460.3271.2570.995100
2.06-2.1161.06325770.8520.2731.0980.992100
2.1-2.1516.80.87325990.9160.2180.91.033100
2.15-2.217.20.68925950.9560.1690.711.02999.9
2.2-2.2517.20.59125720.9550.1450.6091.046100
2.25-2.31160.47426040.9650.1210.4891.067100
2.31-2.3818.30.40426000.9830.0960.4151.101100
2.38-2.4618.30.33625810.9850.080.3451.102100
2.46-2.5418.10.29226150.9880.070.31.147100
2.54-2.6517.70.22726190.9910.0550.2331.187100
2.65-2.7716.90.17426200.9940.0430.181.28799.9
2.77-2.9117.10.1426120.9960.0340.1441.335100
2.91-3.118.20.11426290.9970.0270.1181.397100
3.1-3.33180.08826360.9980.0210.0911.483100
3.33-3.6716.60.07226540.9980.0180.0751.4999.9
3.67-4.218.20.0626510.9990.0140.0621.405100
4.2-5.2917.20.05427010.9990.0130.0551.43399.9
5.29-49.6716.30.04928460.9990.0120.0511.55499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WZU

6wzu


Resolution: 1.95→49.67 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.999 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 2620 5 %RANDOM
Rwork0.1749 ---
obs0.1757 49570 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 45.533 Å2 / Biso min: 27.49 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å20 Å2
2--1.12 Å2-0 Å2
3----2.24 Å2
Refinement stepCycle: final / Resolution: 1.95→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 57 230 2780
Biso mean--50.08 52.46 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132682
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172412
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.6743655
X-RAY DIFFRACTIONr_angle_other_deg1.3661.5835637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70223.74131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49515458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.588159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023010
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02562
LS refinement shellResolution: 1.953→2.004 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 157 -
Rwork0.309 3334 -
all-3491 -
obs--91.1 %
Refinement TLS params.Method: refined / Origin x: 49.413 Å / Origin y: 37.787 Å / Origin z: 14.493 Å
111213212223313233
T0.0517 Å20.0121 Å20.0062 Å2-0.0601 Å20.0333 Å2--0.0455 Å2
L0.6517 °2-0.3385 °2-0.0834 °2-1.3386 °20.0181 °2--0.9287 °2
S0.0612 Å °-0.0124 Å °0.0812 Å °-0.0512 Å °-0.1598 Å °-0.0786 Å °0.0387 Å °0.0517 Å °0.0986 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 315
2X-RAY DIFFRACTION1A501 - 511

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