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- PDB-6mea: Crystal structure of a Tylonycteris bat coronavirus HKU4 macrodom... -

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Entry
Database: PDB / ID: 6mea
TitleCrystal structure of a Tylonycteris bat coronavirus HKU4 macrodomain in complex with adenosine diphosphate ribose (ADP-ribose)
ComponentsReplicase polyprotein 1ab
KeywordsHYDROLASE / Coronavirus / Macrodomain / ADP-ribose / ADP-ribosylhydrolase
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / single-stranded RNA binding / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 ...RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesBat coronavirus HKU4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHammond, R.G. / Schormann, N. / McPherson, R.L. / Leung, A.K.L. / Deivanayagam, C.C.S. / Johnson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119456 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: ADP-Ribose and Analogues bound to the DeMARylating Macrodomain from the Bat Coronavirus HKU4
Authors: Hammond, R.G. / Schormann, N. / McPherson, R.L. / Leung, A.K.L. / Deivanayagam, C. / Johnson, M.A.
History
DepositionSep 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 13, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,3094
Polymers37,1902
Non-polymers1,1192
Water6,702372
1
A: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1542
Polymers18,5951
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1542
Polymers18,5951
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.614, 41.642, 59.783
Angle α, β, γ (deg.)73.160, 88.290, 88.250
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 18595.129 Da / Num. of mol.: 2 / Fragment: macrodomain (UNP residues 1154-1324)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bat coronavirus HKU4 / Gene: rep, 1a-1b / Plasmid: pET15b-TEV / Cell line (production host): BL21(DE3)pLysS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C6W3
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEG3350, 0.1 M HEPES, pH 7.0-7.5, protein:ligand molar ratio 1:10
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 2, 2017 / Details: Mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→39.85 Å / Num. obs: 63312 / % possible obs: 92.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 10 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.074 / Rrim(I) all: 0.142 / Net I/σ(I): 9.8
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 3 / Num. unique obs: 2865 / CC1/2: 0.662 / Rpim(I) all: 0.421 / Rrim(I) all: 0.783 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSVersion Nov. 1, 2016data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5DUS

5dus


Resolution: 1.35→33.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.586 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 3225 5.1 %RANDOM
Rwork0.142 ---
obs0.1431 60045 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.5 Å2 / Biso mean: 14.8 Å2 / Biso min: 3.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.11 Å20.04 Å2
2--0.11 Å20.02 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.35→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 72 372 2870
Biso mean--9.74 29.02 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192577
X-RAY DIFFRACTIONr_bond_other_d0.0020.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9523528
X-RAY DIFFRACTIONr_angle_other_deg0.93135528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36825.588102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22415407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.602156
X-RAY DIFFRACTIONr_chiral_restr0.3980.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
X-RAY DIFFRACTIONr_rigid_bond_restr4.25634955
X-RAY DIFFRACTIONr_sphericity_free19.9025209
X-RAY DIFFRACTIONr_sphericity_bonded8.14355083
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 217 -
Rwork0.279 4335 -
all-4552 -
obs--89.82 %

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