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Entry
Database: PDB / ID: 5s3l
TitlePanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 Nsp3 macrodomain in complex with Z54628578
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / SARS-CoV-2 Nsp3 macrodomain
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / exoribonuclease complex / viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / exoribonuclease complex / viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA cap binding complex / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Lyases; Phosphorus-oxygen lyases / positive regulation of RNA biosynthetic process / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / RNA-templated transcription / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive regulation of viral genome replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Non-structural protein NSP15, middle domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / NSP1 globular domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / NSP1, globular domain, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus Nsp3d Ubl domain profile. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus replicase NSP4, N-terminal / Coronavirus papain-like peptidase / Coronavirus replicase NSP6 / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP3, C-terminal / Coronavirus endopeptidase C30 / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, N-terminal, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus
Similarity search - Domain/homology
N-methylpyrimidin-2-amine / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.091 Å
AuthorsFearon, D. / Schuller, M. / Rangel, V.L. / Douangamath, A. / Rack, J.G.M. / Zhu, K. / Aimon, A. / Brandao-Neto, J. / Dias, A. / Dunnet, L. ...Fearon, D. / Schuller, M. / Rangel, V.L. / Douangamath, A. / Rack, J.G.M. / Zhu, K. / Aimon, A. / Brandao-Neto, J. / Dias, A. / Dunnet, L. / Gorrie-Stone, T.J. / Powell, A.J. / Krojer, T. / Skyner, R. / Thompson, W. / Ahel, I. / von Delft, F.
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
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2021Provider: 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 1.2Jul 7, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)36,4673
Polymers36,3582
Non-polymers1091
Water8,593477
1
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2882
Polymers18,1791
Non-polymers1091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)88.130, 88.130, 39.214
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 / Fragment: macrodomain
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, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-JH4 / N-methylpyrimidin-2-amine


Mass: 109.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.09 Å3/Da / Density % sol: 41.27 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 0.1 / Details: 30% PEG 3K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 1.08→88.14 Å / Num. obs: 128892 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Rrim(I) all: 0.108 / Net I/σ(I): 5.4 / Num. measured all: 695465 / Scaling rejects: 1027
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.08-1.13.21.4981997462150.4010.9591.7880.497.2
5.92-88.146.70.0657728580.9950.0260.06617.2100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (20-MAY-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6WOJ
Resolution: 1.091→88.13 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.04 / SU Rfree Blow DPI: 0.045 / SU Rfree Cruickshank DPI: 0.042
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 4561 4.83 %RANDOM
Rwork0.1604 ---
obs0.1621 94341 75.3 %-
Displacement parametersBiso max: 66.42 Å2 / Biso mean: 19.09 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.7677 Å20 Å20 Å2
2--1.7677 Å20 Å2
3----3.5354 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.091→88.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 8 477 3012
Biso mean--18.35 30.42 -
Num. residues----334
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d903SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it2639HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion341SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3112SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2647HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3609HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.23
X-RAY DIFFRACTIONt_other_torsion15.29
LS refinement shellResolution: 1.09→1.2 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2377 91 4.82 %
Rwork0.2531 1796 -
all-1887 -
obs--6.26 %

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