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- EMDB-1240: The structure of a filamentous bacteriophage. -

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Basic information

Entry
Database: EMDB / ID: EMD-1240
TitleThe structure of a filamentous bacteriophage.
Map dataThis is the volume generated by IHRSR. To align with PDB 2hi5, use "CP TO BRIX" in SPIDER, with 2.4 A/pixel, and default unit cell.
Sample
  • Sample: bacteriophage fd
  • Protein or peptide: pVIII
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesEnterobacteria phage fd (virus)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 8.0 Å
AuthorsWang YA / Yu X / Overman S / Tsuboi M / Thomas GJ / Egelman EH
CitationJournal: J Mol Biol / Year: 2006
Title: The structure of a filamentous bacteriophage.
Authors: Ying A Wang / Xiong Yu / Stacy Overman / Masamichi Tsuboi / George J Thomas / Edward H Egelman /
Abstract: Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure ...Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure of such filaments have depended upon techniques such as modeling or X-ray fiber diffraction, given that direct visualization of the subunit organization has not been possible. We report the first image reconstruction of a filamentous virus, bacteriophage fd, by cryoelectron microscopy. Although these thin ( approximately 70 A in diameter) rather featureless filaments scatter weakly, we have been able to achieve a nominal resolution of approximately 8 A using an iterative helical reconstruction procedure. We show that two different conformations of the virus exist, and that in both states the subunits are packed differently than in conflicting models previously proposed on the basis of X-ray fiber diffraction or solid-state NMR studies. A significant fraction of the population of wild-type fd is either disordered or in multiple conformational states, while in the presence of the Y21M mutation, this heterogeneity is greatly reduced, consistent with previous observations. These results show that new computational approaches to helical reconstruction can greatly extend the ability to visualize heterogeneous protein polymers at a reasonably high resolution.
History
DepositionJul 12, 2006-
Header (metadata) releaseJul 12, 2006-
Map releaseSep 14, 2006-
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: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2hi5
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2hi5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1240.gif

Downloads & links

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Map

FileDownload / File: emd_1240.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the volume generated by IHRSR. To align with PDB 2hi5, use "CP TO BRIX" in SPIDER, with 2.4 A/pixel, and default unit cell.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.4 Å/pix.
x 100 pix.
= 240. Å		2.4 Å/pix.
x 100 pix.
= 240. Å		2.4 Å/pix.
x 100 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0352 / Movie #1: 0.1
Minimum - Maximum-0.25674 - 0.364415
Average (Standard dev.)0.00493299 (±0.0356837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 240 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z240.000240.000240.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.2570.3640.005

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Supplemental data

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Sample components

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Entire : bacteriophage fd

EntireName: bacteriophage fd (virus)
Components
  • Sample: bacteriophage fd
  • Protein or peptide: pVIII

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Supramolecule #1000: bacteriophage fd

SupramoleculeName: bacteriophage fd / type: sample / ID: 1000 / Oligomeric state: polymer of single protein / Number unique components: 1

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Macromolecule #1: pVIII

MacromoleculeName: pVIII / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Enterobacteria phage fd (virus) / synonym: bacteriophage fd
Molecular weightExperimental: 5207 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

StainingType: NEGATIVE / Details: unstained
VitrificationCryogen name: ETHANE / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 67 / Bits/pixel: 14
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 50000
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 37.4 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR
CTF correctionDetails: each film

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Atomic model buiding 1

Initial modelPDB ID:

2hi5


Chain - Chain ID: A
Detailsmanual docking with chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2hi5:
Model for bacteriophage fd from cryo-EM

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