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Yorodumi- EMDB-6560: Bacteriophage phi29 prohead particle stalled during DNA packaging -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6560 | |||||||||
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Title | Bacteriophage phi29 prohead particle stalled during DNA packaging | |||||||||
Map data | Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP | |||||||||
Sample |
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Keywords | bacteriophage phi29 / ATPase / DNA packaging motor | |||||||||
Biological species | Bacillus phage phi29 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Mao H / Saha M / Reyes-Aldrete E / Sherman M / Woodson M / Jardine PJ / Grimes S / Morais M | |||||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor. Authors: Huzhang Mao / Mitul Saha / Emilio Reyes-Aldrete / Michael B Sherman / Michael Woodson / Rockney Atz / Shelley Grimes / Paul J Jardine / Marc C Morais / Abstract: Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline ...Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6560.map.gz | 29.8 MB | EMDB map data format | |
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Header (meta data) | emd-6560-v30.xml emd-6560.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | 400_6560.gif 80_6560.gif | 64.5 KB 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6560 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6560 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6560.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.94 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Reconstruction of bacteriophage phi29 stalled during DNA packagin...
Entire | Name: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction. |
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Components |
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-Supramolecule #1000: Reconstruction of bacteriophage phi29 stalled during DNA packagin...
Supramolecule | Name: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. Only particles that had clearly packaged DNA were included in the reconstruction. type: sample / ID: 1000 Oligomeric state: The particle is based on a prolate icosahedron with T = 3, Q = 5 quasi-symmetry wherein one pentameric capsomer at one end of the particle is replaced by a dodecameric gp10 ...Oligomeric state: The particle is based on a prolate icosahedron with T = 3, Q = 5 quasi-symmetry wherein one pentameric capsomer at one end of the particle is replaced by a dodecameric gp10 connector protein and a pentameric pRNA and gp16 ATPase ring. Number unique components: 1 |
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-Supramolecule #1: Bacillus phage phi29
Supramolecule | Name: Bacillus phage phi29 / type: virus / ID: 1 / Name.synonym: bacteriophage phi29 Details: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. After two minutes incubation, DNAses were added to remove unpackaged DNA. Only particles ...Details: Reconstruction of bacteriophage phi29 stalled during DNA packaging via the addition of gamma-S-ATP. After two minutes incubation, DNAses were added to remove unpackaged DNA. Only particles that had clearly packaged were included in the reconstruction. NCBI-ID: 10756 / Sci species name: Bacillus phage phi29 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: bacteriophage phi29 |
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Host (natural) | Organism: Bacillus subtilis (bacteria) / synonym: BACTERIA(EUBACTERIA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 / Details: 25 mM Tris-HCl, 5 mM MgCl2, 50 mM NaCl |
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Grid | Details: Quantifoil holey carbon on top of 200 mesh copper grid, plasma-cleaned |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER Method: Blot from behind the sample for 4 seconds before plunging. |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Specialist optics | Energy filter - Name: JEOL |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | Jun 24, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25 e/Å2 |
-Image processing
CTF correction | Details: Each Micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: EMAN Details: C5 symmetry was imposed in all stages of the reconstruction, with the 5-fold axis along Z. The final map was low-pass filtered at 14 Angstrom. Number images used: 1871 |
Details | The particles were selected using semi-automatic particle selection, followed by manual deletion of bad particles and manual selection of missed particles. |