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Entry
Database: PDB / ID: 5rve
TitlePanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000736709772
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / HYDROLASE / Macrodomain / ADP-ribose / SARS-CoV-2
Function / homology
Function and homology information


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 ...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 / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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
Chem-W8A / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsCorrey, G.J. / Young, I.D. / Thompson, M.C. / Fraser, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation2031205 United States
CitationJournal: Sci Adv / Year: 2021
Title: Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Authors: Schuller, M. / Correy, G.J. / Gahbauer, S. / Fearon, D. / Wu, T. / Diaz, R.E. / Young, I.D. / Carvalho Martins, L. / Smith, D.H. / Schulze-Gahmen, U. / Owens, T.W. / Deshpande, I. / Merz, G. ...Authors: Schuller, M. / Correy, G.J. / Gahbauer, S. / Fearon, D. / Wu, T. / Diaz, R.E. / Young, I.D. / Carvalho Martins, L. / Smith, D.H. / Schulze-Gahmen, U. / Owens, T.W. / Deshpande, I. / Merz, G.E. / Thwin, A.C. / Biel, J.T. / Peters, J.K. / Moritz, M. / Herrera, N. / Kratochvil, H.T. / Aimon, A. / Bennett, J.M. / Brandao Neto, J. / Cohen, A.E. / Dias, A. / Douangamath, A. / Dunnett, L. / Fedorov, O. / Ferla, M.P. / Fuchs, M.R. / Gorrie-Stone, T.J. / Holton, J.M. / Johnson, M.G. / Krojer, T. / Meigs, G. / Powell, A.J. / Rack, J.G.M. / Rangel, V.L. / Russi, S. / Skyner, R.E. / Smith, C.A. / Soares, A.S. / Wierman, J.L. / Zhu, K. / O'Brien, P. / Jura, N. / Ashworth, A. / Irwin, J.J. / Thompson, M.C. / Gestwicki, J.E. / von Delft, F. / Shoichet, B.K. / Fraser, J.S. / Ahel, I.
History
DepositionSep 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_ec / _entity_name_com.name
Revision 1.2May 12, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_type
Revision 1.3Jun 9, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 25, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5903
Polymers36,3582
Non-polymers2321
Water9,422523
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4112
Polymers18,1791
Non-polymers2321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,1791
Polymers18,1791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.728, 88.728, 39.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Non-structural protein 3 / Nsp3 / PL2-PRO / Papain-like protease / Papain-like proteinase / PL-PRO


Mass: 18178.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HIS6 purification tag and linker (MHHHHHHSSGVDLGTENLYFQ) cleaved with TEV protease
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pET22b(+) / 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-W8A / {[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid


Mass: 232.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 100 mM CHES, 28% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 1→39.68 Å / Num. obs: 165537 / % possible obs: 99.7 % / Redundancy: 6.392 % / Biso Wilson estimate: 13.917 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.862 / Net I/σ(I): 18.76 / Num. measured all: 1058038
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1-1.065.650.6422.0514853126751262890.870.70898.3
1.06-1.136.3630.3314.3715995525139251390.9680.361100
1.13-1.236.6510.1957.5815565123404234030.9890.211100
1.23-1.346.4240.12811.2613826021524215240.9940.139100
1.34-1.56.8180.08717.7913311319527195230.9970.094100
1.5-1.736.5520.05529.0111316117275172720.9980.059100
1.73-2.126.6330.03844.139690814618146100.9990.04299.9
2.12-36.2990.03155.397157311373113630.9990.03399.9
3-39.686.3740.02562.4540886642764140.9990.02899.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDS0.94data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→39.68 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 7995 4.83 %
Rwork0.1575 157507 -
obs0.1581 165502 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.04 Å2 / Biso mean: 17.6499 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 26 523 3080
Biso mean--47.08 28.83 -
Num. residues----336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.010.2562660.31544976524294
1.01-1.020.27332370.26495046528398
1.02-1.040.26222600.233952915551100
1.04-1.050.23822670.21351805447100
1.05-1.060.20373230.199252225545100
1.06-1.080.22922480.190852255473100
1.08-1.090.21662700.177852425512100
1.09-1.110.20042430.167352395482100
1.11-1.130.19082860.167552405526100
1.13-1.150.17272350.16352385473100
1.15-1.170.18622620.153753075569100
1.17-1.190.18232690.15852465515100
1.19-1.210.18772930.150151815474100
1.21-1.230.17612290.147953255554100
1.23-1.260.16842600.154751985458100
1.26-1.290.17262770.14952825559100
1.29-1.320.16992850.1552445529100
1.32-1.360.16332780.15252335511100
1.36-1.40.17712470.150252585505100
1.4-1.440.16062690.151852575526100
1.44-1.490.14622530.149253045557100
1.49-1.550.16072760.144752105486100
1.55-1.630.16762650.143452845549100
1.63-1.710.17522630.144853115574100
1.71-1.820.16842530.153652815534100
1.82-1.960.15182790.15352915570100
1.96-2.160.14352860.153252795565100
2.16-2.470.14552870.148653045591100
2.47-3.110.17632600.157553285588100
3.11-39.680.17572690.160354855754100

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