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- EMDB-1012: Minor proteins, mobile arms and membrane-capsid interactions in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-1012
TitleMinor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Map dataThis is a map of the sus607 mutant
Sample
  • Sample: Bacteriophage PRD1 sus607 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: 13.4 Å
AuthorsSan Martin C / Huiskonen JT / Bamford JK / Butcher SJ / Fuller SD / Bamford DH / Burnett RM
CitationJournal: Nat Struct Biol / Year: 2002
Title: Minor proteins, mobile arms and membrane-capsid interactions in the bacteriophage PRD1 capsid.
Authors: Carmen San Martín / Juha T Huiskonen / Jaana K H Bamford / Sarah J Butcher / Stephen D Fuller / Dennis H Bamford / Roger M Burnett /
Abstract: Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the ...Bacteriophage PRD1 shares many structural and functional similarities with adenovirus. A major difference is the PRD1 internal membrane, which acts in concert with vertex proteins to translocate the phage genome into the host. Multiresolution models of the PRD1 capsid, together with genetic analyses, provide fine details of the molecular interactions associated with particle stability and membrane dynamics. The N- and C-termini of the major coat protein (P3), which are required for capsid assembly, act as conformational switches bridging capsid to membrane and linking P3 trimers. Electrostatic P3-membrane interactions increase virion stability upon DNA packaging. Newly revealed proteins suggest how the metastable vertex works and how the capsid edges are stabilized.
History
Header (metadata) releaseMay 25, 2002-
DepositionOct 9, 2002-
Map releaseOct 10, 2002-
UpdateJun 29, 2016-
Current statusJun 29, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9697.761559063
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 9697.761559063
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1gw8
  • Surface level: 9697.761559063
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1gw8
  • Surface level: 11047.988358153
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1gw8
  • 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_1012.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the sus607 mutant
Voxel sizeX=Y=Z: 3.42 Å
Density
Contour Level1: 8520.0 / Movie #1: 9697.7615591
Minimum - Maximum-20774.400000000001455 - 27000.0
Average (Standard dev.)283.963999999999999 (±4049.909999999999854)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions256256256
Spacing256256256
CellA=B=C: 875.52 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z875.520875.520875.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS256256256
D min/max/mean-20774.36326999.969283.964

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Supplemental data

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Sample components

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Entire : Bacteriophage PRD1 sus607 mutant

EntireName: Bacteriophage PRD1 sus607 mutant
Components
  • Sample: Bacteriophage PRD1 sus607 mutant
  • Virus: Enterobacteria phage PRD1 (virus)

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Supramolecule #1000: Bacteriophage PRD1 sus607 mutant

SupramoleculeName: Bacteriophage PRD1 sus607 mutant / type: sample / ID: 1000
Details: The sample is a virion containing at least 19 structural proteins and a double stranded DNA genome. This map is from the sus607 mutant and lacks protein P11
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: No / Syn species name: bacteriophage PRD1
Host (natural)Organism: Salmonella enterica (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: capsid (contains proteins P3 and P30) / 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 1 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: 4.13 µm / Nominal defocus min: 0.77 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 105 K
DateNov 1, 2001
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 15 / 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 .01
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.4 Å / Resolution method: OTHER / Software - Name: EMBL-ICOS, MRC
Details: final maps were calculated by making a normalized sum of seperate ctf multiplied maps Baker, T. S., Olson, N. H., and Fuller, S. D. (1999). Adding the third dimension to virus life cycles: ...Details: final maps were calculated by making a normalized sum of seperate ctf multiplied maps 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: 1729
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
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: ridgid body. The scale of the map and the effective resolution were determined from a comparison between the P3 portion of the sus607 reconstruction and the atomic model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 100 / Target criteria: minimizing R factor (final 47.7%)
Output model

PDB-1gw8:
quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography.

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