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Yorodumi- PDB-6q67: Crystal structure of porcine ACBD3 GOLD domain in complex with 3A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q67 | ||||||
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Title | Crystal structure of porcine ACBD3 GOLD domain in complex with 3A protein of Aichivirus C | ||||||
Components |
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Keywords | VIRAL PROTEIN / complex / aichivirus / picornavirus | ||||||
Function / homology | Function and homology information RNA-protein covalent cross-linking / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity ...RNA-protein covalent cross-linking / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Aichivirus C | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 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 | 6q67.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q67.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 6q67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q67_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 6q67_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 6q67_validation.xml.gz | 7.8 KB | Display | |
Data in CIF | 6q67_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q67 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q67 | HTTPS FTP |
-Related structure data
Related structure data | 6q68C 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: 19486.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DUB6 |
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#2: Protein/peptide | Mass: 3759.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aichivirus C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B8R1T8*PLUS |
#3: Sugar | ChemComp-BGC / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % |
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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, 20mM L-arginine, 20mM L-threonine, 20mM L-histidine, 20mM betaine, 10mM trans-4-hydroxy-L- ...Details: 15% w/v PEG 3000, 10% v/v 1,4-butanediol, 1% w/v N,N-dimethyldodecylamine-N-oxide , 10% w/v glucose, 20mM L-arginine, 20mM L-threonine, 20mM L-histidine, 20mM betaine, 10mM trans-4-hydroxy-L-proline, 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: Mar 2, 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: 2.249→47.97 Å / Num. obs: 14951 / % possible obs: 99.07 % / Redundancy: 5.8 % / Biso Wilson estimate: 68.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03611 / Rrim(I) all: 0.0399 / Net I/σ(I): 21.49 |
Reflection shell | Resolution: 2.249→2.328 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 1448 / CC1/2: 0.799 / % possible all: 97.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LZ1 Resolution: 2.249→47.969 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.249→47.969 Å
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Refine LS restraints |
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LS refinement shell |
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