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- PDB-7jme: Structure of the SARS-CoV-2 NSP3 Macro X domain in complex with c... -

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Basic information

Entry
Database: PDB / ID: 7jme
TitleStructure of the SARS-CoV-2 NSP3 Macro X domain in complex with cyclic AMP
ComponentsNon-structural protein 3
KeywordsVIRAL PROTEIN/INHIBITOR / macro domain / cAMP / cyclic AMP / viral protein / sars-cov-2 / VIRAL PROTEIN-INHIBITOR complex
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 / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 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 ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / 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 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / regulation of autophagy / 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 / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / 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
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 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 / 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 replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsVuksanovic, N. / Melkonian, T.R. / Silvaggi, N.R.
CitationJournal: Slas Discov / Year: 2020
Title: Discovery of Drug-Like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3.
Authors: Virdi, R.S. / Bavisotto, R.V. / Hopper, N.C. / Vuksanovic, N. / Melkonian, T.R. / Silvaggi, N.R. / Frick, D.N.
History
DepositionJul 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 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 1.2Sep 15, 2021Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,8232
Polymers18,4941
Non-polymers3291
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.210, 33.036, 60.476
Angle α, β, γ (deg.)90.000, 96.351, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Non-structural protein 3 / NSP3 / PL2-PRO / Papain-like protease / Papain-like proteinase / PL-PRO


Mass: 18494.109 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 (bacteria) / Variant (production host): Star
References: UniProt: P0DTD1, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 4K, 0.1M MES pH 6.5, crystals then soaked in 35% PEG 4K, 20mM cAMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→24.7 Å / Num. obs: 20508 / % possible obs: 95.05 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.0764 / Rpim(I) all: 0.04878 / Rrim(I) all: 0.09095 / Net I/σ(I): 10.91
Reflection shellResolution: 1.55→1.606 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 4.23 / Num. unique obs: 1938 / CC1/2: 0.891 / Rpim(I) all: 0.1822 / Rrim(I) all: 0.3442

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6wey

6wey


Resolution: 1.55→24.7 Å / SU ML: 0.1015 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1821 1998 9.78 %
Rwork0.1568 18453 -
obs0.1593 20433 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 22 135 1395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821298
X-RAY DIFFRACTIONf_angle_d0.89341775
X-RAY DIFFRACTIONf_chiral_restr0.0566210
X-RAY DIFFRACTIONf_plane_restr0.0055229
X-RAY DIFFRACTIONf_dihedral_angle_d20.3159463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.19561240.17691145X-RAY DIFFRACTION84.83
1.59-1.630.20211450.17491336X-RAY DIFFRACTION95.24
1.63-1.680.18981430.16771312X-RAY DIFFRACTION96.49
1.68-1.730.21621410.1611313X-RAY DIFFRACTION94.91
1.73-1.790.22431450.16041331X-RAY DIFFRACTION97.3
1.79-1.860.17831430.15451329X-RAY DIFFRACTION95.65
1.86-1.950.17041450.15741326X-RAY DIFFRACTION95.4
1.95-2.050.18651420.15391309X-RAY DIFFRACTION95.21
2.05-2.180.19371430.1491331X-RAY DIFFRACTION95.59
2.18-2.350.17271450.14641337X-RAY DIFFRACTION95.67
2.35-2.590.18731490.15521366X-RAY DIFFRACTION98.19
2.59-2.960.17341480.15211374X-RAY DIFFRACTION98.7
2.96-3.730.17371510.14651393X-RAY DIFFRACTION97.78
3.73-24.70.17391360.17181251X-RAY DIFFRACTION86.31
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.728973396150.6715363727820.2428088076222.42875303020.7705337212421.119264743960.09152935306420.564144206794-0.252510967274-0.4727033389680.0468726469724-0.1523390391820.09385849107520.302190812523-0.09025622778060.2207619349330.03553255412430.0101243328830.176012933794-0.05176622725530.1226114885846.12211715377-9.280741614735.81669449134
23.903682420830.1913604674730.6003065331492.29794465606-0.04251051108633.28709450610.248954704049-0.459357856198-0.2315264439260.180763175602-0.0260531846322-0.414387913550.007692376093430.318249892259-0.196231688150.0950376826345-0.0320701076303-0.01540656443280.189192113812-0.01208307247040.17024535353317.0404670649-4.6608695820423.150006134
33.228404540150.371782813290.720653440071.995115075010.9817527827913.432755581390.0387731811573-0.17908635550.194631622544-0.118566969150.0772743516771-0.177692808508-0.2173564336830.425431024259-0.129533309770.11840127918-0.0293083490670.01977742154890.103102216198-0.01424619674650.11008235330213.24556371780.19034162630718.3053300816
44.483906005440.953500079709-2.560919298454.035684364-1.064309736385.55159686502-0.0297954465693-0.563397666537-0.09789844462950.243019139929-0.09815907415180.125476585281-0.160899909365-0.09968071259340.06794556226490.09679685978380.004274677637860.006837259408040.171823637429-0.007801731233090.05706783521393.58802789504-3.9039297108424.4142599779
53.45753189641.52139739712-0.7995449241327.61125442079-3.263004644657.330128712220.0265156249245-0.2220562900650.3697675928270.01919927455910.01769404771040.301810555305-0.484091917119-0.461546821551-0.1544128872730.1259972350670.0441387007076-0.01943481623610.115818269831-0.05094944376290.1388910553-1.582466881941.2684019185118.1467878422
63.611045564090.846763970736-0.6623471787011.913415190040.785300804943.136253773760.01018044131270.0623560033097-0.0878211281879-0.0985869062001-0.09042567183610.1677354610480.0275887286353-0.1077087315310.04015871959510.09696477739150.0252392465304-0.009581414023340.0614667688577-0.01463223444880.0855267426984-0.540218640474-6.9291990734613.640800759
75.732081109931.266175840382.657039620140.907881462678-1.268182390956.721948984680.004482351302370.182351862059-0.113707873965-0.2063207854860.02741048894190.4784680495150.22314005542-0.3818371584820.1050358171860.2001621812590.00844507354392-0.0369272363370.102943488903-0.03654762882530.216901660449-6.25676693139-17.41463476369.77636710995
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 208 through 242 )208 - 2421 - 35
22chain 'A' and (resid 243 through 276 )243 - 27636 - 69
33chain 'A' and (resid 277 through 294 )277 - 29470 - 87
44chain 'A' and (resid 295 through 309 )295 - 30988 - 102
55chain 'A' and (resid 310 through 322 )310 - 322103 - 115
66chain 'A' and (resid 323 through 361 )323 - 361116 - 154
77chain 'A' and (resid 362 through 373 )362 - 373155 - 167

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