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- EMDB-5149: P22 Procapsid Shell -

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Basic information

Entry
Database: EMDB / ID: EMD-5149
TitleP22 Procapsid Shell
Map dataThis is a density map of WT P22 procapsid shells (devoid of scaffolding protein)
Sample
  • Sample: P22 Procapsid Shell
  • Virus: Enterobacteria phage P22 (virus)
KeywordsPrecursor capsid structure for bacteriophage P22
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / viral procapsid / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsParent KN / Khayat R / Tu LH / Suhanovsky MM / Coritnes JR / Teschke CM / Johnson JE / Baker TS
CitationJournal: Structure / Year: 2010
Title: P22 coat protein structures reveal a novel mechanism for capsid maturation: stability without auxiliary proteins or chemical crosslinks.
Authors: Kristin N Parent / Reza Khayat / Long H Tu / Margaret M Suhanovsky / Juliana R Cortines / Carolyn M Teschke / John E Johnson / Timothy S Baker /
Abstract: Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, ...Viral capsid assembly and stability in tailed, dsDNA phage and Herpesviridae are achieved by various means including chemical crosslinks (unique to HK97), or auxiliary proteins (lambda, T4, phi29, and herpesviruses). All these viruses have coat proteins (CP) with a conserved, HK97-like core structure. We used a combination of trypsin digestion, gold labeling, cryo-electron microscopy, 3D image reconstruction, and comparative modeling to derive two independent, pseudoatomic models of bacteriophage P22 CP: before and after maturation. P22 capsid stabilization results from intersubunit interactions among N-terminal helices and an extensive "P loop," which obviate the need for crosslinks or auxiliary proteins. P22 CP also has a telokin-like Ig domain that likely stabilizes the monomer fold so that assembly may proceed via individual subunit addition rather than via preformed capsomers as occurs in HK97. Hence, the P22 CP structure may be a paradigm for understanding how monomers assemble in viruses like phi29 and HSV-1.
History
DepositionDec 10, 2009-
Header (metadata) releaseJan 6, 2010-
Map releaseJan 6, 2010-
UpdateJun 21, 2010-
Current statusJun 21, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyi
  • Surface level: 1.45
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5149_1.tif

Downloads & links

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Map

FileDownload / File: emd_5149.map.gz / Format: CCP4 / Size: 296.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a density map of WT P22 procapsid shells (devoid of scaffolding protein)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 430 pix.
= 696.6 Å		1.62 Å/pix.
x 430 pix.
= 696.6 Å		1.62 Å/pix.
x 430 pix.
= 696.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.45 / Movie #1: 1.45
Minimum - Maximum-4.16424 - 7.5243
Average (Standard dev.)0.000000000054544 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-214-214-214
Dimensions430430430
Spacing430430430
CellA=B=C: 696.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z430430430
origin x/y/z0.0000.0000.000
length x/y/z696.600696.600696.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-214-214-214
NC/NR/NS430430430
D min/max/mean-4.1647.5240.000

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Supplemental data

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Sample components

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Entire : P22 Procapsid Shell

EntireName: P22 Procapsid Shell
Components
  • Sample: P22 Procapsid Shell
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: P22 Procapsid Shell

SupramoleculeName: P22 Procapsid Shell / type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: Phage P22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: Phage P22
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: P22 Procapsid shell / Diameter: 580 Å / T number (triangulation number): 7

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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

Concentration8 mg/mL
BufferpH: 7.6 / Details: 20 mM sodium phosphate
GridDetails: Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunge-freezer / Method: Blot for 2-3 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: at working magnification
DateAug 10, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 164 / Average electron dose: 8 e/Å2 / Details: scanned on Nikon SuperCool 8000 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.65 µm / Nominal defocus min: 0.41 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Polrar Multi Specimen Holder / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Detailsdata were collected on film
CTF correctionDetails: ROBEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 11997

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