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- EMDB-1101: Coat protein fold and maturation transition of bacteriophage P22 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1101
TitleCoat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.
Map dataZ-axis along 3fold symmetry axis, Y-axis along 2fold symmetry axis
Sample
  • Sample: P22 Mature Phage
  • Virus: Enterobacteria phage P22 (virus)
Biological speciesEnterobacteria phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsJiang W / Li Z / Zhang Z / Baker ML / Prevelige PE / Chiu W
CitationJournal: Nat Struct Biol / Year: 2003
Title: Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions.
Authors: Wen Jiang / Zongli Li / Zhixian Zhang / Matthew L Baker / Peter E Prevelige / Wah Chiu /
Abstract: Bacteriophage P22 is a prototypical biological machine used for studying protein complex assembly and capsid maturation. Using cryo-EM, we solved the structures of P22 before and after the capsid ...Bacteriophage P22 is a prototypical biological machine used for studying protein complex assembly and capsid maturation. Using cryo-EM, we solved the structures of P22 before and after the capsid maturation at 8.5 A and 9.5 A resolutions, respectively. These structures allowed visualization of alpha-helices and beta-sheets from which the capsid protein fold is derived. The capsid fold is similar to that of the coat protein of HK97 bacteriophage. The cryo-EM shows that a large conformational change of the P22 capsid during maturation transition involves not only the domain movement of individual subunits, but also refolding of the capsid protein.
History
DepositionNov 17, 2004-
Header (metadata) releaseDec 13, 2004-
Map releaseDec 13, 2004-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1101.gif

Downloads & links

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Map

FileDownload / File: emd_1101.map.gz / Format: CCP4 / Size: 116.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZ-axis along 3fold symmetry axis, Y-axis along 2fold symmetry axis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.82 Å/pix.
x 199 pix.
= 361.185 Å		1.82 Å/pix.
x 397 pix.
= 720.555 Å		1.82 Å/pix.
x 397 pix.
= 720.555 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.815 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 3.27 / Movie #1: 3
Minimum - Maximum-8.788 - 12.0128
Average (Standard dev.)0.175442 (±1.58435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-198-1980
Dimensions397397199
Spacing397397199
CellA: 720.555 Å / B: 720.555 Å / C: 361.185 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.8151.8151.815
M x/y/z397397199
origin x/y/z0.0000.0000.000
length x/y/z720.555720.555361.185
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-198-1980
NC/NR/NS397397199
D min/max/mean-8.78812.0130.175

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Supplemental data

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Sample components

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Entire : P22 Mature Phage

EntireName: P22 Mature Phage
Components
  • Sample: P22 Mature Phage
  • Virus: Enterobacteria phage P22 (virus)

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Supramolecule #1000: P22 Mature Phage

SupramoleculeName: P22 Mature Phage / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 18 MDa / Theoretical: 18 MDa

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Supramolecule #1: Enterobacteria phage P22

SupramoleculeName: Enterobacteria phage P22 / type: virus / ID: 1 / Name.synonym: P22 mature phage / Details: the icosahedral protein shell / NCBI-ID: 10754 / Sci species name: Enterobacteria phage P22 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: P22 mature phage
Host (natural)Organism: Salmonella (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 18 MDa / Theoretical: 18 MDa
Virus shellShell ID: 1 / Name: capsid shell / Diameter: 700 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

GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made plunger

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Electron microscopy

MicroscopeJEOL 4000EX
TemperatureMin: 95 K / Max: 95 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: by monitoring Thon rings at very close to focus
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 100 / Average electron dose: 30 e/Å2
Details: scanned at 7micrometer then averaged to 14micrometer step size
Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 5.6 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: per micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SAVR / Number images used: 5600

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Atomic model buiding 1

Initial modelPDB ID:

1fh6
PDB Unreleased entry


Chain - Chain ID: A
SoftwareName: foldhunter
DetailsPDBEntryID_givenInChain. Protocol: rigid body
RefinementProtocol: RIGID BODY FIT / Target criteria: correlation coefficient

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