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Yorodumi- PDB-6q68: Crystal structure of bovine ACBD3 GOLD domain in complex with 3A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q68 | ||||||
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Title | Crystal structure of bovine ACBD3 GOLD domain in complex with 3A protein of enterovirus-F2 (fusion protein) | ||||||
Components |
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Keywords | VIRAL PROTEIN / complex / enterovirus / picornavirus | ||||||
Function / homology | Function and homology information Golgi Associated Vesicle Biogenesis / : / fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / : / protein kinase A regulatory subunit binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane ...Golgi Associated Vesicle Biogenesis / : / fatty-acyl-CoA binding / RNA-protein covalent cross-linking / : / : / protein kinase A regulatory subunit binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / Golgi membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Enterovirus F | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.161 Å | ||||||
Authors | Smola, M. / Boura, E. / Klima, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Arch. Virol. / Year: 2020 Title: Structural basis for hijacking of the host ACBD3 protein by bovine and porcine enteroviruses and kobuviruses. Authors: Smola, M. / Horova, V. / Boura, E. / Klima, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q68.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q68.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 6q68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q68_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 6q68_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 6q68_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 6q68_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q68 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q68 | HTTPS FTP |
-Related structure data
Related structure data | 6q67C 6q69C 5lz1S 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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Unit cell |
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-Components
#1: Protein | Mass: 19304.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ACBD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F1MRE5 #2: Protein/peptide | Mass: 5452.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus F / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q2LKY9, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase #3: Sugar | |
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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: 3.11 Å3/Da / Density % sol: 60.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 15% w/v PEG 3000, 10% v/v 1,4-butanediol, 1% w/v N,N-dimethyldodecylamine-N-oxide , 10% w/v glucose, 4% v/v 1,2-propandiol, 100mM BES/TEA pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 3.161→48.49 Å / Num. obs: 10318 / % possible obs: 99.78 % / Redundancy: 7.5 % / Biso Wilson estimate: 114.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07812 / Rrim(I) all: 0.08403 / Net I/σ(I): 16.06 |
Reflection shell | Resolution: 3.161→3.274 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 1049 / CC1/2: 0.662 / % possible all: 99.24 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LZ1 Resolution: 3.161→48.49 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 112.9 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.161→48.49 Å
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Refine LS restraints |
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LS refinement shell |
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