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Yorodumi- PDB-5j37: Crystal structure of 60-mer BFDV Capsid Protein in complex with s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j37 | ||||||
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Title | Crystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA | ||||||
Components |
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Keywords | VIRUS/DNA / BFDV Virus Capsid Jelly Roll / VIRAL PROTEIN / VIRUS-DNA complex | ||||||
Function / homology | Function and homology information viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | Beak and feather disease virus synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sarker, S. / Raidal, S. / Aragao, D. / Forwood, J.K. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Structural insights into the assembly and regulation of distinct viral capsid complexes. Authors: Subir Sarker / María C Terrón / Yogesh Khandokar / David Aragão / Joshua M Hardy / Mazdak Radjainia / Manuel Jiménez-Zaragoza / Pedro J de Pablo / Fasséli Coulibaly / Daniel Luque / ...Authors: Subir Sarker / María C Terrón / Yogesh Khandokar / David Aragão / Joshua M Hardy / Mazdak Radjainia / Manuel Jiménez-Zaragoza / Pedro J de Pablo / Fasséli Coulibaly / Daniel Luque / Shane R Raidal / Jade K Forwood / Abstract: The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from ...The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from the smallest and simplest known viruses capable of autonomously replicating in animal cells, circoviruses, to establish structural and mechanistic insights into capsid morphogenesis and regulation. The beak and feather disease virus, like many circoviruses, encode only two genes: a capsid protein and a replication initiation protein. The capsid protein forms distinct macromolecular assemblies during replication and here we elucidate these structures at high resolution, showing that these complexes reverse the exposure of the N-terminal arginine rich domain responsible for DNA binding and nuclear localization. We show that assembly of these complexes is regulated by single-stranded DNA (ssDNA), and provide a structural basis of capsid assembly around single-stranded DNA, highlighting novel binding interfaces distinct from the highly positively charged N-terminal ARM domain. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j37.cif.gz | 422.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j37.ent.gz | 345.2 KB | Display | PDB format |
PDBx/mmJSON format | 5j37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/5j37 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/5j37 | HTTPS FTP |
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-Related structure data
Related structure data | 8306C 5j09SC 5j36C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 30237.316 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Beak and feather disease virus / Gene: Cap / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023R6W2 #2: DNA chain | Mass: 9105.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-PO4 / #4: 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: 2.84 Å3/Da / Density % sol: 56.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.8 M Na/K hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40.218 Å / Num. obs: 101384 / % possible obs: 100 % / Redundancy: 8.6 % / Net I/σ(I): 7.5 |
-Processing
Software | Name: PHENIX / Version: (1.10pre_2104: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J09 Resolution: 2.3→40.218 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→40.218 Å
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Refine LS restraints |
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LS refinement shell |
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