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- EMDB-1751: P22 F170L C9 polyheads -

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Basic information

Entry
Database: EMDB / ID: EMD-1751
TitleP22 F170L C9 polyheads
Map dataThis is a helical reconstruction of P22 polyheads with C9 symmetry
Sample
  • Sample: F170L coat protein in C9 helical lattice
  • Virus: Enterobacteria phage P22 (virus)
Keywordscryo-TEM / image reconstruction / helical reconstruction / bacteriophage P22 / virus assembly / coat protein
Biological speciesEnterobacteria phage P22 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsParent KN / Sinkovits RS / Suhanovsky MM / Teschke CM / Egelman EH / Baker TS
CitationJournal: Phys Biol / Year: 2010
Title: Cryo-reconstructions of P22 polyheads suggest that phage assembly is nucleated by trimeric interactions among coat proteins.
Authors: Kristin N Parent / Robert S Sinkovits / Margaret M Suhanovsky / Carolyn M Teschke / Edward H Egelman / Timothy S Baker /
Abstract: Bacteriophage P22 forms an isometric capsid during normal assembly, yet when the coat protein (CP) is altered at a single site, helical structures (polyheads) also form. The structures of three ...Bacteriophage P22 forms an isometric capsid during normal assembly, yet when the coat protein (CP) is altered at a single site, helical structures (polyheads) also form. The structures of three distinct polyheads obtained from F170L and F170A variants were determined by cryo-reconstruction methods. An understanding of the structures of aberrant assemblies such as polyheads helps to explain how amino acid substitutions affect the CP, and these results can now be put into the context of CP pseudo-atomic models. F170L CP forms two types of polyhead and each has the CP organized as hexons (oligomers of six CPs). These hexons have a skewed structure similar to that in procapsids (precursor capsids formed prior to dsDNA packaging), yet their organization differs completely in polyheads and procapsids. F170A CP forms only one type of polyhead, and though this has hexons organized similarly to hexons in F170L polyheads, the hexons are isometric structures like those found in mature virions. The hexon organization in all three polyheads suggests that nucleation of procapsid assembly occurs via a trimer of CP monomers, and this drives formation of a T = 7, isometric particle. These variants also form procapsids, but they mature quite differently: F170A expands spontaneously at room temperature, whereas F170L requires more energy. The P22 CP structure along with scaffolding protein interactions appear to dictate curvature and geometry in assembled structures and residue 170 significantly influences both assembly and maturation.
History
DepositionJun 11, 2010-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateApr 20, 2016-
Current statusApr 20, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.225
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.225
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1751.png

Downloads & links

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Map

FileDownload / File: emd_1751.map.gz / Format: CCP4 / Size: 173.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a helical reconstruction of P22 polyheads with C9 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 360 pix.
= 677.88 Å		1.88 Å/pix.
x 360 pix.
= 677.88 Å		1.88 Å/pix.
x 360 pix.
= 677.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.883 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225 / Movie #1: 0.225
Minimum - Maximum-0.85971999 - 1.0587548
Average (Standard dev.)0.00605284 (±0.19375603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 677.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8831.8831.883
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z677.880677.880677.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.8601.0590.006

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Supplemental data

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Sample components

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Entire : F170L coat protein in C9 helical lattice

EntireName: F170L coat protein in C9 helical lattice
Components
  • Sample: F170L coat protein in C9 helical lattice
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: F170L coat protein in C9 helical lattice

SupramoleculeName: F170L coat protein in C9 helical lattice / type: sample / ID: 1000
Details: This sample was generated by concentrating coat protein monomers
Oligomeric state: Hexon / Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: P22 coat protein / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: P22 coat protein
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 47 MDa / Theoretical: 47 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration35 mg/mL
BufferpH: 7.6 / Details: 20 mM sodium phosphate
GridDetails: Lacey-carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunge-freezer / Method: Blot for 5 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Working magnification
DateOct 10, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 1.883 µm / Number real images: 1141 / Average electron dose: 19 e/Å2 / Od range: 1.5 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 79666 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.96 µm / Nominal defocus min: 0.91 µm / Nominal magnification: 79666
Sample stageSpecimen holder: Polara Multi Specimen Holder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThis reconstruction was done with the iterative helical real space reconstruction method
Final reconstructionApplied symmetry - Helical parameters - Δz: 104 Å
Applied symmetry - Helical parameters - Δ&Phi: 19 °
Applied symmetry - Helical parameters - Axial symmetry: C9 (9 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: IHRSR
CTF correctionDetails: ROBEM

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