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- EMDB-1824: Structural basis for scaffolding-mediated assembly and maturation... -

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Basic information

Entry
Database: EMDB / ID: EMD-1824
TitleStructural basis for scaffolding-mediated assembly and maturation of a dsDNA virus
Map dataThis is the icosahedral density map for bacteriophage P22 procapsid solved by cryo-EM at 3.8-Angstrom resolution
Sample
  • Sample: Bacteriophage P22 procapsid
  • Virus: Enterobacteria phage P22 (virus)
Keywordsbacteriophage / phage / P22 / procapsid / scaffolding / cryo-EM / icosahedral reconstruction / assembly / maturation / dsDNA virus
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 / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen D-H / Baker ML / Hryc CF / DiMaio F / Jakana J / Wu W / Dougherty M / Haase-Pettingell C / Schmid MF / Jiang W ...Chen D-H / Baker ML / Hryc CF / DiMaio F / Jakana J / Wu W / Dougherty M / Haase-Pettingell C / Schmid MF / Jiang W / Baker D / King JA / Chiu W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.
Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / ...Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / Jonathan A King / Wah Chiu /
Abstract: Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This ...Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a model system for this study in the past several decades. However, how capsid assembly is initiated, where and how scaffolding proteins bind to coat proteins in the procapsid, and the conformational changes upon capsid maturation still remain elusive. Here, we report Cα backbone models for the P22 procapsid and infectious virion derived from electron cryomicroscopy density maps determined at 3.8- and 4.0-Å resolution, respectively, and the first procapsid structure at subnanometer resolution without imposing symmetry. The procapsid structures show the scaffolding protein interacting electrostatically with the N terminus (N arm) of the coat protein through its C-terminal helix-loop-helix motif, as well as unexpected interactions between 10 scaffolding proteins and the 12-fold portal located at a unique vertex. These suggest a critical role for the scaffolding proteins both in initiating the capsid assembly at the portal vertex and propagating its growth on a T = 7 icosahedral lattice. Comparison of the procapsid and the virion backbone models reveals coordinated and complex conformational changes. These structural observations allow us to propose a more detailed molecular mechanism for the scaffolding-mediated capsid assembly initiation including portal incorporation, release of scaffolding proteins upon DNA packaging, and maturation into infectious virions.
History
DepositionNov 19, 2010-
Header (metadata) releaseDec 10, 2010-
Map releaseJan 28, 2011-
UpdateNov 26, 2014-
Current statusNov 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xyy
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xyy
  • 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_1824.map.gz / Format: CCP4 / Size: 2.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the icosahedral density map for bacteriophage P22 procapsid solved by cryo-EM at 3.8-Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 864 pix.
= 915.84 Å
1.06 Å/pix.
x 864 pix.
= 915.84 Å
1.06 Å/pix.
x 864 pix.
= 915.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.63474905 - 4.04660702
Average (Standard dev.)0.0003842 (±0.17108497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-432-432-432
Dimensions864864864
Spacing864864864
CellA=B=C: 915.83997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z864864864
origin x/y/z0.0000.0000.000
length x/y/z915.840915.840915.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-70-70-70
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS-432-432-432
NC/NR/NS864864864
D min/max/mean-1.6354.0470.000

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Supplemental data

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Sample components

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Entire : Bacteriophage P22 procapsid

EntireName: Bacteriophage P22 procapsid
Components
  • Sample: Bacteriophage P22 procapsid
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: Bacteriophage P22 procapsid

SupramoleculeName: Bacteriophage P22 procapsid / type: sample / ID: 1000
Details: This sample is wild-type P22 procapsid containing the portal and the scaffolding proteins, but the capsid shell has icosahedral symmetry
Number unique components: 1

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: P22 / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: P22
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Diameter: 610 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

Concentration1 mg/mL
BufferpH: 7.6 / Details: 50 mM Tris pH 7.6, 25 mM NaCl, 2mM EDTA
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4.2 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3000SFF
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.6 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Top entry / Specimen holder model: JEOL
TemperatureMin: 4.2 K / Max: 4.2 K / Average: 4.2 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
DateMar 7, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 277 / Average electron dose: 36 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: EMAN:az, alt, phi
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 23400
DetailsThe particles were selected using an automatic selection program

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