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- EMDB-1507: cryoEM structure of bacteriophage lambda procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-1507
TitlecryoEM structure of bacteriophage lambda procapsid
Map datalambda prohead reconstruction
Sample
  • Sample: lambda procapsid
  • Virus: Enterobacteria phage lambda (virus)
Keywordsbacteriophage / phage / procapsid / prophage / lambda / icosahedral / cryoEM
Biological speciesEnterobacteria phage lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.5 Å
AuthorsLander GC / Evilevitch A / Jeembaeva M / Potter CS / Carragher B / Johnson JE
CitationJournal: Structure / Year: 2008
Title: Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM.
Authors: Gabriel C Lander / Alex Evilevitch / Meerim Jeembaeva / Clinton S Potter / Bridget Carragher / John E Johnson /
Abstract: We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid ...We report the cryo-EM structure of bacteriophage lambda and the mechanism for stabilizing the 20-A-thick capsid containing the dsDNA genome. The crystal structure of the HK97 bacteriophage capsid fits most of the T = 7 lambda particle density with only minor adjustment. A prominent surface feature at the 3-fold axes corresponds to the cementing protein gpD, which is necessary for stabilization of the capsid shell. Its position coincides with the location of the covalent cross-link formed in the docked HK97 crystal structure, suggesting an evolutionary replacement of this gene product in lambda by autocatalytic chemistry in HK97. The crystal structure of the trimeric gpD, in which the 14 N-terminal residues required for capsid binding are disordered, fits precisely into the corresponding EM density. The N-terminal residues of gpD are well ordered in the cryo-EM density, adding a strand to a beta-sheet formed by the capsid proteins and explaining the mechanism of particle stabilization.
History
DepositionApr 15, 2008-
Header (metadata) releaseApr 15, 2008-
Map releaseMar 31, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 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

1507.gif

Downloads & links

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Map

FileDownload / File: emd_1507.map.gz / Format: CCP4 / Size: 105.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlambda prohead reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 192 pix.
= 433.92 Å		2.26 Å/pix.
x 384 pix.
= 867.84 Å		2.26 Å/pix.
x 384 pix.
= 867.84 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: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 2.57 / Movie #1: 3
Minimum - Maximum-4.97389 - 18.814399999999999
Average (Standard dev.)0.332316 (±0.895572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-96
Dimensions384384192
Spacing384384192
CellA: 867.84 Å / B: 867.84 Å / C: 433.92 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z384384192
origin x/y/z0.0000.0000.000
length x/y/z867.840867.840433.920
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-192-192-96
NC/NR/NS384384192
D min/max/mean-4.97418.8140.332

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Supplemental data

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Sample components

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Entire : lambda procapsid

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

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Supramolecule #1000: lambda procapsid

SupramoleculeName: lambda procapsid / type: sample / ID: 1000
Details: particles were present in a preparation of a 37.7 kbp packaging lambda mutant
Oligomeric state: icosahedral / Number unique components: 1
Molecular weightExperimental: 16 MDa / Theoretical: 16 MDa

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Supramolecule #1: Enterobacteria phage lambda

SupramoleculeName: Enterobacteria phage lambda / type: virus / ID: 1 / Name.synonym: capsid, gpE / NCBI-ID: 10710 / Sci species name: Enterobacteria phage lambda / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: capsid, gpE
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 16 MDa / Theoretical: 16 MDa
Virus shellShell ID: 1 / Name: gpE / Diameter: 500 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

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: 10mM MgSO4, 50mM Tris-HCl
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: double blot for 7 seconds

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 77 K / Max: 78 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 135,000 times magnification
DateFeb 16, 2007
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 2683 / Average electron dose: 19 e/Å2 / Camera length: 61.4
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side-entry cryostage / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Detailsparticles selected using a template-based algorithm, then centered using EMAN cenalignint
CTF correctionDetails: phases of each particle flipped using values estimated automatically from the micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: OTHER / Software - Name: EMAN
Details: Amplitudes of final reconstruction adjusted using SPIDER to fit the density Fourier amplitudes to an experimental 1D low-angle X-ray scattering curve
Number images used: 4640
Final angle assignmentDetails: EMAN icos
Final two d classificationNumber classes: 379

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Atomic model buiding 1

Initial modelPDB ID:

3bqw

SoftwareName: UCSF Chimera
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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