[English] 日本語
Yorodumi- EMDB-1013: Combined EM/X-ray imaging yields a quasi-atomic model of the aden... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1013 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. | |||||||||
Map data | This is the map of the sus 1 mutant and three orthogonal sections. The map has been limited to 14 angstroms resolution and scaled to an amplitude profile of the atomic model of the P3 portion of the shell. | |||||||||
Sample |
| |||||||||
Function / homology | Bacteriophage PRD1, P3 / Bacteriophage PRD1, P3, N-terminal / P3 major capsid protein / Group II dsDNA virus coat/capsid protein / Viral coat protein subunit / viral capsid / Major capsid protein P3 Function and homology information | |||||||||
Biological species | Enterobacteria phage PRD1 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
Authors | San Martin C / Burnett RM / de Haas F / Heinkel R / Rutten T / Fuller SD / Butcher SJ / Bamford DH | |||||||||
Citation | Journal: Structure / Year: 2001 Title: Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Authors: C S Martín / R M Burnett / F de Haas / R Heinkel / T Rutten / S D Fuller / S J Butcher / D H Bamford / Abstract: BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A ...BACKGROUND: The dsDNA bacteriophage PRD1 has a membrane inside its icosahedral capsid. While its large size (66 MDa) hinders the study of the complete virion at atomic resolution, a 1.65-A crystallographic structure of its major coat protein, P3, is available. Cryo-electron microscopy (cryo-EM) and three-dimensional reconstruction have shown the capsid at 20-28 A resolution. Striking architectural similarities between PRD1 and the mammalian adenovirus indicate a common ancestor. RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking ...RESULTS: The P3 atomic structure has been fitted into improved cryo-EM reconstructions for three types of PRD1 particles: the wild-type virion, a packaging mutant without DNA, and a P3-shell lacking the membrane and the vertices. Establishing the absolute EM scale was crucial for an accurate match. The resulting "quasi-atomic" models of the capsid define the residues involved in the major P3 interactions, within the quasi-equivalent interfaces and with the membrane, and show how these are altered upon DNA packaging. CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations ...CONCLUSIONS: The new cryo-EM reconstructions reveal the structure of the PRD1 vertex and the concentric packing of DNA. The capsid is essentially unchanged upon DNA packaging, with alterations limited to those P3 residues involved in membrane contacts. These are restricted to a few of the N termini along the icosahedral edges in the empty particle; DNA packaging leads to a 4-fold increase in the number of contacts, including almost all copies of the N terminus and the loop between the two beta barrels. Analysis of the P3 residues in each quasi-equivalent interface suggests two sites for minor proteins in the capsid edges, analogous to those in adenovirus. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1013.map.gz | 28.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1013-v30.xml emd-1013.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
Images | 1013.gif | 32.4 KB | ||
Others | emd_1013_additional_1.map.gz emd_1013_additional_2.map.gz emd_1013_additional_3.map.gz | 166 KB 165.9 KB 171.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1013 | HTTPS FTP |
-Validation report
Summary document | emd_1013_validation.pdf.gz | 293.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1013_full_validation.pdf.gz | 292.3 KB | Display | |
Data in XML | emd_1013_validation.xml.gz | 6.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1013 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1013 | HTTPS FTP |
-Related structure data
Related structure data | 1hb7MC 1hb9MC 1014C 1hb5C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_1013.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | This is the map of the sus 1 mutant and three orthogonal sections. The map has been limited to 14 angstroms resolution and scaled to an amplitude profile of the atomic model of the P3 portion of the shell. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Supplemental map: emd 1013 additional 1.map
File | emd_1013_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: emd 1013 additional 2.map
File | emd_1013_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: emd 1013 additional 3.map
File | emd_1013_additional_3.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Bacteriophage PRD1 sus1 mutant
Entire | Name: Bacteriophage PRD1 sus1 mutant |
---|---|
Components |
|
-Supramolecule #1000: Bacteriophage PRD1 sus1 mutant
Supramolecule | Name: Bacteriophage PRD1 sus1 mutant / type: sample / ID: 1000 Details: The sample is a mutant virion containing at least 18 structural proteins. This mutant does not package the dsDNA genome. Oligomeric state: A pseudo T=25 assembly / Number unique components: 1 |
---|---|
Molecular weight | Theoretical: 70 MDa |
-Supramolecule #1: Enterobacteria phage PRD1
Supramolecule | Name: Enterobacteria phage PRD1 / type: virus / ID: 1 / Name.synonym: bacteriophage PRD1 / Details: a T=25 virion / NCBI-ID: 10658 / Sci species name: Enterobacteria phage PRD1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: bacteriophage PRD1 |
---|---|
Host (natural) | Organism: Salmonella enterica (bacteria) / synonym: BACTERIA(EUBACTERIA) |
Virus shell | Shell ID: 1 / Name: capsid (P8 and P30 shell) / Diameter: 70 Å / T number (triangulation number): 25 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.2 / Details: 20 mM Tris HCl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 23 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: EMBL plunger. vitrification carried out at 23 degrees at ambient humidity Method: Blot for 2 s before plunging into ethane slush |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG/ST |
---|---|
Temperature | Average: 105 K |
Details | the images are taken a underfocused although the entry indicates a positive defocus value |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 29 / Average electron dose: 6 e/Å2 / Camera length: 44 Details: images were scanned at 7 micron steps size and then averaged to give a final size of 14 microns Od range: 1 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 36000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were purified by rate-zonal centrifugation and ion-exchange chromatography Walin,Tuma,Thomas and Bamford Virology (1994) 201:1-7 |
---|---|
CTF correction | Details: normalized sum of ctf multiplied images |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: EMBL-ICOS, MRC Details: final maps were calculated as a normalized sum of image ffts using the svd versions of matbg and then normalized using an overall profile de Haas, F., Paatero, A. O., Mindich,L., Bamford, D. ...Details: final maps were calculated as a normalized sum of image ffts using the svd versions of matbg and then normalized using an overall profile de Haas, F., Paatero, A. O., Mindich,L., Bamford, D. H. and Fuller, S. D. (1999). A symmetry mismatch at the site of RNA packaging by the polymerase complex of dsRNA bacteriophage phi-6. Journal of Molecular Biology 294, 357-372. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T. and Fuller, S. D. (2000). Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Molecular Cell 5, 255-266. San Martin, C., Burnett, R. M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S. D., Butcher, S. J. and Bamford, D. H. (2001). Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure (Camb) 9, 917-30. Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs. Microbiology and Molecular Biology Reviews 63, 862-922. Butcher, S. J., Bamford, D. H., and Fuller, S. D. (1995). DNA packaging orders the membrane of bacteriophage PRD1. Embo J 14, 6078-6086. Ferlenghi, I., Gowen, B., de Haas, F., Mancini, E. J., Garoff, H., Sjoberg, M., and Fuller, S. D. (1998). The first step: activation of the Semliki Forest virus spike protein precursor causes a localized conformational change in the trimeric spike. J Mol Biol 283, 71-81. Fuller, S. D., Berriman, J. A., Butcher, S. J., and Gowen, B. E. (1995). Low pH induces swiveling of the glycoprotein heterodimers in the Semliki Forest virus spike complex. Cell 81, 715-725. Fuller, S. D., Butcher, S. J., Cheng, R. H., and Baker, T. S. (1996). Three-dimensional reconstruction of icosahedral particles--the uncommon line. J Struct Biol 116, 48-55. Mancini, E. J., Clarke, M., Gowen, B., Rutten, T., and Fuller, S. D. (2000). Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Molecular Cell 5, 255-266. Mancini, E. J., de Haas, F., and Fuller, S. D. (1997). High-resolution icosahedral reconstruction: fulfilling the promise of cryo-electron microscopy. Structure 5, 741-750. San Martin, C., Burnett,R. M., de Haas, F., Heinkel, R., Rutten, T., Fuller, S. D., Butcher, S. J., and Bamford, D. H. (2001). Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure (Camb) 9, 917-930. San Martin, C., Huiskonen, J. T., Bamford, J. K., Butcher, S. J., Fuller, S. D., Bamford, D. H., and Burnett, R. M. (2002). Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid. Nat Struct Biol 9, 756-763. Sheehan, B., Fuller, S. D., Pique, M. E., and Yeager, M. (1996). AVS software for visualization in molecular microscopy. J Struct Biol 116, 99-106. Number images used: 1800 |
Final angle assignment | Details: range giving min eigenvalues for inversion of less than 0.01 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L |
---|---|
Software | Name: X-plor and emfit (M. Rossmann Cheng, R., Kuhn, R., Olson, N., Rossmann, M., and Baker, T. (1995). Nucleocapsid and glycoprotein organization in an enveloped virus. Cell 80, 621-630.) |
Details | Protocol: rigid body refinement. The amplitude and distance scales were determined by comparison with an initial quasi atomic model |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 150 / Target criteria: minimizing R factor and clashes |
Output model | PDB-1hb7: PDB-1hb9: |