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- PDB-6z72: SARS-CoV-2 Macrodomain in complex with ADP-HPM -

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Basic information

Entry
Database: PDB / ID: 6z72
TitleSARS-CoV-2 Macrodomain in complex with ADP-HPM
ComponentsReplicase polyprotein 1ab
KeywordsVIRAL PROTEIN / Viral Macrodomain / ADP-ribose binding module / ADP-ribosylhydrolase / ADP-ribosylation / ADP-HPM
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 / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / 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 / lipid binding / DNA-templated transcription / 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 Nonstructural protein 13, 1B domain ...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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 Interface domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) 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 / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / : / Coronavirus 3Ecto domain profile. / 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 (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Peptidase family C16 domain profile.
Similarity search - Domain/homology
Chem-A3R / D-MALATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZorzini, V. / Rack, J. / Ahel, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101794 and 210634 United Kingdom
CitationJournal: Open Biology / Year: 2020
Title: Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential.
Authors: Rack, J.G.M. / Zorzini, V. / Zhu, Z. / Schuller, M. / Ahel, D. / Ahel, I.
History
DepositionMay 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1ab
B: Replicase polyprotein 1ab
C: Replicase polyprotein 1ab
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,68020
Polymers75,9154
Non-polymers2,76616
Water5,260292
1
A: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7146
Polymers18,9791
Non-polymers7365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5904
Polymers18,9791
Non-polymers6113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6525
Polymers18,9791
Non-polymers6734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7245
Polymers18,9791
Non-polymers7454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.811, 83.126, 84.276
Angle α, β, γ (deg.)90.000, 94.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 208 through 232 or (resid 233...
21(chain B and (resid 208 through 259 or (resid 260...
31(chain D and (resid 208 through 232 or (resid 233...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYS(chain A and (resid 208 through 232 or (resid 233...AA208 - 2325 - 29
12LYSLYSLYSLYS(chain A and (resid 208 through 232 or (resid 233...AA23330
13GLUGLULYSLYS(chain A and (resid 208 through 232 or (resid 233...AA206 - 3793 - 176
14GLUGLULYSLYS(chain A and (resid 208 through 232 or (resid 233...AA206 - 3793 - 176
15GLUGLULYSLYS(chain A and (resid 208 through 232 or (resid 233...AA206 - 3793 - 176
16GLUGLULYSLYS(chain A and (resid 208 through 232 or (resid 233...AA206 - 3793 - 176
17GLUGLULYSLYS(chain A and (resid 208 through 232 or (resid 233...AA206 - 3793 - 176
21ASNASNLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB208 - 2595 - 56
22ALAALAALAALA(chain B and (resid 208 through 259 or (resid 260...BB26057
23VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
24VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
25VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
26VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
27VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
28VALVALLYSLYS(chain B and (resid 208 through 259 or (resid 260...BB207 - 3794 - 176
31ASNASNLYSLYS(chain D and (resid 208 through 232 or (resid 233...DD208 - 2325 - 29
32LYSLYSLYSLYS(chain D and (resid 208 through 232 or (resid 233...DD23330
33VALVALGLUGLU(chain D and (resid 208 through 232 or (resid 233...DD207 - 3784 - 175
34VALVALGLUGLU(chain D and (resid 208 through 232 or (resid 233...DD207 - 3784 - 175
35VALVALGLUGLU(chain D and (resid 208 through 232 or (resid 233...DD207 - 3784 - 175
36VALVALGLUGLU(chain D and (resid 208 through 232 or (resid 233...DD207 - 3784 - 175

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


Mass: 18978.633 Da / Num. of mol.: 4
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, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 5 types, 308 molecules

#2: Chemical
ChemComp-A3R / Adenosine Diphosphate (Hydroxymethyl)pyrrolidine monoalcohol


Mass: 526.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N6O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.775 M DL-Malic Acid pH 7.0 4.5% (v/v) ethylene glycol 200 mM potassium cyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.3→50.5 Å / Num. obs: 36664 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 28.76 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.164 / Rrim(I) all: 0.232 / Net I/σ(I): 3.2 / Num. measured all: 71830
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.3820.828700235490.6550.8281.172198.8
8.91-50.51.80.02812416710.9980.0280.0399.399.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.6.3data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Z5T

6z5t


Resolution: 2.3→50.499 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2632 1825 5.02 %
Rwork0.218 34519 -
obs0.2202 36344 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.63 Å2 / Biso mean: 43.2715 Å2 / Biso min: 13.26 Å2
Refinement stepCycle: final / Resolution: 2.3→50.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 177 292 5548
Biso mean--45.47 39.38 -
Num. residues----693
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2194X-RAY DIFFRACTION9.468TORSIONAL
12B2194X-RAY DIFFRACTION9.468TORSIONAL
13D2194X-RAY DIFFRACTION9.468TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.36220.33531200.303258597
2.3622-2.43170.35451100.3016265399
2.4317-2.51020.32681280.2952269099
2.5102-2.59990.30991340.2815262999
2.5999-2.7040.30011350.2736264799
2.704-2.8270.30151400.2627265099
2.827-2.97610.27951600.2396261299
2.9761-3.16250.26671610.2326263999
3.1625-3.40660.2541310.2066265999
3.4066-3.74940.24921610.19252648100
3.7494-4.29160.23741710.17812670100
4.2916-5.4060.21761230.16872715100
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)
11.90830.07940.87320.9452-0.04380.64730.0624-0.06930.06230.0903-0.0864-0.0087-0.03030.02040.01550.2928-0.00330.0590.41960.00571.08451.1449-12.4143.6137
21.31560.02720.03420.093-0.080.61830.03850.0256-0.0655-0.0084-0.0047-0.03970.06770.08620.0060.28660.01010.03090.42150.00231.11730.9634-7.336-3.7151
31.8678-0.52280.06473.76820.33871.05840.052-0.0552-0.1157-0.06050.013-0.0768-0.07450.0831-0.05310.1538-0.0202-0.00780.13730.00580.36054.317812.5546-38.4423
41.96530.6342-0.80764.4043-0.0451.1250.0405-0.0045-0.2115-0.1844-0.10520.2028-0.00890.03730.04650.18660.0052-0.05330.12650.01640.231834.069217.7634-45.5855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A206 - 379
2X-RAY DIFFRACTION2chain 'B'B207 - 379
3X-RAY DIFFRACTION3chain 'C'C206 - 379
4X-RAY DIFFRACTION4chain 'D'D207 - 378

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