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Open data
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Basic information
Entry | Database: PDB / ID: 4k7h | ||||||
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Title | Major capsid protein P1 of the Pseudomonas phage phi6 | ||||||
![]() | Major inner protein P1 | ||||||
![]() | VIRAL PROTEIN / major capsid protein | ||||||
Function / homology | : / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Boura, E. / Nemecek, D. / Plevka, P. / Steven, C.A. / Hurley, J.H. | ||||||
![]() | ![]() Title: Subunit folds and maturation pathway of a dsRNA virus capsid. Authors: Daniel Nemecek / Evzen Boura / Weimin Wu / Naiqian Cheng / Pavel Plevka / Jian Qiao / Leonard Mindich / J Bernard Heymann / James H Hurley / Alasdair C Steven / ![]() Abstract: The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits ...The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 711.8 KB | Display | ![]() |
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PDB format | ![]() | 596.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.4 KB | Display | ![]() |
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Full document | ![]() | 591 KB | Display | |
Data in XML | ![]() | 134.5 KB | Display | |
Data in CIF | ![]() | 179.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 85835.453 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 HEPES, pH 7.5, 180 mM calcium acetate, 10 mM EDTA, 39% PEG 400, 1:1 molar mixture with P7 protein, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97899 Å / Relative weight: 1 |
Reflection | Resolution: 3.596→42 Å / Num. all: 73087 / Num. obs: 66561 / % possible obs: 91.07 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Net I/σ(I): 11.15 |
Reflection shell | Resolution: 3.596→3.66 Å / Mean I/σ(I) obs: 2.04 / % possible all: 41.67 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: cryoEM map Resolution: 3.5964→40.92 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 29.94 / 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: 3.5964→40.92 Å
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Refine LS restraints |
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LS refinement shell |
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