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Yorodumi- PDB-6meb: Crystal structure of Tylonycteris bat coronavirus HKU4 macrodomai... -
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-Basic information
Entry | Database: PDB / ID: 6meb | ||||||
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Title | Crystal structure of Tylonycteris bat coronavirus HKU4 macrodomain in complex with nicotinamide adenine dinucleotide (NAD+) | ||||||
Components | Replicase polyprotein 1ab | ||||||
Keywords | HYDROLASE / 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 / 5'-3' DNA helicase activity / 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 ISG15-protein conjugation / G-quadruplex RNA binding ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / 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 ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / 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 / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Bat coronavirus HKU4 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hammond, R.G. / Schormann, N. / McPherson, R.L. / Leung, A.K.L. / Deivanayagam, C.C.S. / Johnson, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6meb.cif.gz | 141.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6meb.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 6meb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6meb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6meb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6meb_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6meb_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/6meb ftp://data.pdbj.org/pub/pdb/validation_reports/me/6meb | HTTPS FTP |
-Related structure data
Related structure data | 6meaSC 6menC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 310 - 468 / Label seq-ID: 6 - 164
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2017 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.59 Å / Num. obs: 28245 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.3 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.051 / Rrim(I) all: 0.101 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1381 / CC1/2: 0.905 / Rpim(I) all: 0.118 / Rrim(I) all: 0.206 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6MEA Resolution: 1.8→33.59 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.577 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.1 Å2 / Biso mean: 16.6 Å2 / Biso min: 2.19 Å2
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Refinement step | Cycle: final / Resolution: 1.8→33.59 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4938 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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