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- PDB-44ps: 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal f... -

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Entry
Database: PDB / ID: 44ps
Title6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
ComponentsPapain-like protease nsp3
KeywordsVIRAL PROTEIN / Macrodomain
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / snRNP Assembly ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / snRNP Assembly / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host ISG15-protein conjugation / mRNA guanylyltransferase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / DNA helicase / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell endoplasmic reticulum / symbiont-mediated suppression of host NF-kappaB cascade / 5'-3' RNA polymerase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated perturbation of host ubiquitin-like protein modification / host cell Golgi apparatus / lyase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / methyltransferase cap1 activity / DNA helicase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / lipid binding / RNA-directed RNA polymerase activity / host cell cytoplasm / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / 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 profile. / (+) RNA virus helicase core domain / 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 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus replicase NSP2, N-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 / Peptidase family C16 domain profile. / : / : / Coronavirus Nsp3 ectodomain (3Ecto) profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.77 Å
AuthorsPassmore, S.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT220100405 Australia
Citation
Journal: Biorxiv / Year: 2026
Title: Optimizing the connectivity of protein conformations to untangle ensemble refinement
Authors: Passmore, S.K. / Holton, J.M. / Zatsepin, N.A. / Martin, A.V.
#1: Journal: 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. / OBrien, 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
DepositionAug 8, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Papain-like protease nsp3


Theoretical massNumber of molelcules
Total (without water)18,5481
Polymers18,5481
Non-polymers00
Water46,4972581
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.820, 29.630, 37.960
Angle α, β, γ (deg.)90.000, 103.560, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

21A-832-

HOH

31A-2284-

HOH

41A-2338-

HOH

51A-2523-

HOH

61A-2559-

HOH

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Components

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


Mass: 18548.027 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2581 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 100 mM sodium acetate, 28% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.7292 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7292 Å / Relative weight: 1
ReflectionResolution: 0.73→67.961 Å / Num. obs: 197980 / % possible obs: 93 % / Redundancy: 60.805 % / Biso Wilson estimate: 6.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.117 / Net I/σ(I): 31.52
Reflection shellResolution: 0.77→0.8 Å / Redundancy: 21.54 % / Rmerge(I) obs: 15.598 / Num. unique obs: 17322 / % possible all: 97.25

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Processing

Software
NameVersionClassification
PHENIX2.0_5793refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.77→29.65 Å / SU ML: 0.0541 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 5.5349
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.0641 8709 4.88 %
Rwork0.047 169579 -
obs0.0478 178288 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.7 Å2
Refinement stepCycle: LAST / Resolution: 0.77→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 0 2581 3863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737824
X-RAY DIFFRACTIONf_angle_d1.025310632
X-RAY DIFFRACTIONf_chiral_restr0.08111254
X-RAY DIFFRACTIONf_plane_restr0.00741380
X-RAY DIFFRACTIONf_dihedral_angle_d13.49122796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.77-0.780.28512880.24955361X-RAY DIFFRACTION94.48
0.78-0.790.22332670.21355533X-RAY DIFFRACTION97.84
0.79-0.80.19152820.17615586X-RAY DIFFRACTION99.39
0.8-0.810.15832900.14065637X-RAY DIFFRACTION99.83
0.81-0.820.15852770.12575666X-RAY DIFFRACTION99.98
0.82-0.830.1273100.11455602X-RAY DIFFRACTION99.98
0.83-0.840.10482860.09145640X-RAY DIFFRACTION100
0.84-0.850.10812880.08645596X-RAY DIFFRACTION100
0.85-0.870.09182880.07115673X-RAY DIFFRACTION100
0.87-0.880.08072960.06375642X-RAY DIFFRACTION99.98
0.88-0.90.08162830.05785632X-RAY DIFFRACTION100
0.9-0.910.0822910.05425643X-RAY DIFFRACTION99.98
0.91-0.930.07622860.05195651X-RAY DIFFRACTION99.97
0.93-0.950.06753120.04555636X-RAY DIFFRACTION99.98
0.95-0.970.06152780.04325658X-RAY DIFFRACTION99.98
0.97-0.990.05482890.04015632X-RAY DIFFRACTION100
0.99-1.020.05692860.03935679X-RAY DIFFRACTION100
1.02-1.050.05853010.03795616X-RAY DIFFRACTION100
1.05-1.080.04642900.03555681X-RAY DIFFRACTION99.97
1.08-1.110.04822790.03195673X-RAY DIFFRACTION100
1.11-1.150.04412940.03095698X-RAY DIFFRACTION100
1.15-1.20.03872910.02855643X-RAY DIFFRACTION100
1.2-1.250.04432890.03075659X-RAY DIFFRACTION100
1.25-1.320.04492890.03165683X-RAY DIFFRACTION100
1.32-1.40.04683090.03185697X-RAY DIFFRACTION100
1.4-1.510.05153300.03425643X-RAY DIFFRACTION100
1.51-1.660.05373000.03495723X-RAY DIFFRACTION100
1.66-1.90.05922730.04055724X-RAY DIFFRACTION100
1.9-2.390.06032510.03915803X-RAY DIFFRACTION100
2.39-29.650.06693160.05175869X-RAY DIFFRACTION99.73

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