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- PDB-6xg3: The crystal structure of Papain-Like Protease of SARS CoV-2 , C11... -

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Basic information

Entry
Database: PDB / ID: 6xg3
TitleThe crystal structure of Papain-Like Protease of SARS CoV-2 , C111S mutant, at room temperature
ComponentsNon-structural protein 3
KeywordsHYDROLASE / covid-19 / coronavirus / SARS / CoV-2 / papain-like protease / IDP51000 / Center for Structural Genomics of Infectious Diseases / CSGID
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 / 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 ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / 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 / copper ion binding / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / DNA clamp loader activity / symbiont-mediated suppression of host gene expression / 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
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / 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 ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / 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 / :
Similarity search - Domain/homology
PHOSPHATE ION / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsOsipiuk, J. / Tesar, C. / Jedrzejczak, R. / Endres, M. / 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
DepositionJun 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com
Item: _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name
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 1.3Oct 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: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1244
Polymers35,9281
Non-polymers1963
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: based on visual assessment of crystal packing
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15260 Å2
2
A: Non-structural protein 3
hetero molecules

A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2478
Polymers71,8552
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3110 Å2
ΔGint-11 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.439, 82.439, 135.713
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Non-structural protein 3 / Papain-like protease / pp1ab / ORF1ab polyprotein / nsp3 / PL2-PRO / Papain-like proteinase / PL- ...Papain-like protease / pp1ab / ORF1ab polyprotein / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO / Peptidase C16


Mass: 35927.695 Da / Num. of mol.: 1 / Mutation: C111S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M acetate buffer, 0.8 NaH2PO4/1.2 M K2HPO4

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Data collection

DiffractionMean temperature: 295 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: May 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→49.23 Å / Num. obs: 19357 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.056 / Rrim(I) all: 0.176 / Χ2: 0.985 / Net I/av σ(I): 17.2 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.548.91.6071.49420.5140.571.7070.796100
2.54-2.598.91.3179640.5220.4671.3990.827100
2.59-2.649.51.3299260.6880.4531.4050.821100
2.64-2.6910.21.1899820.7190.3881.2520.843100
2.69-2.7510.51.0559390.7590.3411.110.844100
2.75-2.8210.40.8649380.8510.280.9090.868100
2.82-2.8910.30.7559790.8720.2460.7940.852100
2.89-2.9610.10.639340.9030.2070.6640.882100
2.96-3.059.90.4939550.9450.1630.520.884100
3.05-3.159.40.4029740.9470.1380.4250.901100
3.15-3.269.60.3029420.9710.1020.3190.935100
3.26-3.3910.30.2479610.980.080.260.988100
3.39-3.5510.30.29580.9890.0650.211.022100
3.55-3.7310.20.1669650.9910.0540.1751.023100
3.73-3.979.90.1419810.9930.0470.1481.053100
3.97-4.279.30.1129650.9940.0390.1181.184100
4.27-4.710.30.0939820.9970.030.0981.249100
4.7-5.3810.10.0879900.9970.0290.0921.186100
5.38-6.789.20.08710010.9960.030.0921.113100
6.78-49.239.10.06810790.9970.0240.0721.36899.8

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Processing

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

6wrh


Resolution: 2.48→49.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 14.325 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.193 1004 5.2 %RANDOM
Rwork0.1513 ---
obs0.1535 18320 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.58 Å2 / Biso mean: 55.079 Å2 / Biso min: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.48→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 7 41 2531
Biso mean--63.22 49.99 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132614
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172328
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.6573565
X-RAY DIFFRACTIONr_angle_other_deg1.3161.5715448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.22424.016127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.182157
X-RAY DIFFRACTIONr_chiral_restr0.0660.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
LS refinement shellResolution: 2.48→2.543 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 74 -
Rwork0.293 1133 -
obs--86.21 %
Refinement TLS params.Method: refined / Origin x: 3.5651 Å / Origin y: 80.9974 Å / Origin z: 28.8063 Å
111213212223313233
T0.0477 Å20.0131 Å20.0216 Å2-0.0093 Å20.0014 Å2--0.0242 Å2
L0.9793 °20.032 °20.1574 °2-1.0756 °2-0.5688 °2--1.4276 °2
S0.0205 Å °-0.0381 Å °0.1023 Å °0.0716 Å °0.009 Å °-0.0193 Å °-0.052 Å °-0.0272 Å °-0.0295 Å °

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