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- EMDB-1013: Combined EM/X-ray imaging yields a quasi-atomic model of the aden... -

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Entry
Database: EMDB / ID: EMD-1013
TitleCombined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions.
Map dataThis 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
  • Sample: Bacteriophage PRD1 sus1 mutant
  • Virus: Enterobacteria phage PRD1 (virus)
Function / homologyBacteriophage 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 speciesEnterobacteria phage PRD1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsSan Martin C / Burnett RM / de Haas F / Heinkel R / Rutten T / Fuller SD / Butcher SJ / Bamford DH
CitationJournal: 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
Header (metadata) releaseJun 5, 2002-
DepositionOct 9, 2002-
Map releaseOct 10, 2002-
UpdateAug 12, 2015-
Current statusAug 12, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1hb7
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1hb9
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1hb7
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1hb9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1013.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis 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.
Voxel sizeX=Y=Z: 3.44 Å
Density
Contour Level1: 2.3 / Movie #1: 2.5
Minimum - Maximum-4.7899 - 8.050840000000001
Average (Standard dev.)0.0016896 (±0.999871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions256256256
Spacing256256256
CellA=B=C: 880.64 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.443.443.44
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z880.640880.640880.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS256256256
D min/max/mean-4.7908.0510.002

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Supplemental data

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Sample components

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Entire : Bacteriophage PRD1 sus1 mutant

EntireName: Bacteriophage PRD1 sus1 mutant
Components
  • Sample: Bacteriophage PRD1 sus1 mutant
  • Virus: Enterobacteria phage PRD1 (virus)

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Supramolecule #1000: Bacteriophage PRD1 sus1 mutant

SupramoleculeName: 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 weightTheoretical: 70 MDa

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Supramolecule #1: Enterobacteria phage PRD1

SupramoleculeName: 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 shellShell ID: 1 / Name: capsid (P8 and P30 shell) / Diameter: 70 Å / T number (triangulation number): 25

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2 / Details: 20 mM Tris HCl
VitrificationCryogen 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

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 36000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 105 K
Detailsthe images are taken a underfocused although the entry indicates a positive defocus value
Image recordingCategory: 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

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Image processing

CTF correctionDetails: normalized sum of ctf multiplied images
Final angle assignmentDetails: range giving min eigenvalues for inversion of less than 0.01
Final reconstructionApplied 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
DetailsThe particles were purified by rate-zonal centrifugation and ion-exchange chromatography Walin,Tuma,Thomas and Bamford Virology (1994) 201:1-7

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Atomic model buiding 1

Initial modelPDB 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
SoftwareName: 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.)
DetailsProtocol: rigid body refinement. The amplitude and distance scales were determined by comparison with an initial quasi atomic model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 150 / Target criteria: minimizing R factor and clashes
Output model

PDB-1hb7:
quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography.

PDB-1hb9:
quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography.

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