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- EMDB-5012: Bacteriophage lambda stabilization by auxiliary protein gpD -

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Basic information

Entry
Database: EMDB / ID: EMD-5012
TitleBacteriophage lambda stabilization by auxiliary protein gpD
Map datamature wild type phage lambda
Sample
  • Sample: Mature wild type bacteriophage lambda
  • Virus: Enterobacteria phage (virus)
Keywordsbacteriophage / phage / lambda / icosahedral / capsid / cryoEM
Biological speciesEnterobacteria phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 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 14, 2008-
Header (metadata) releaseApr 17, 2008-
Map releaseApr 22, 2009-
UpdateDec 10, 2009-
Current statusDec 10, 2009Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5012_1.tif

Downloads & links

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Map

FileDownload / File: emd_5012.map.gz / Format: CCP4 / Size: 105.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmature wild type phage lambda
Voxel sizeX=Y=Z: 2.02 Å
Density
Contour Level1: 0.859 / Movie #1: 1.6
Minimum - Maximum-7.06435 - 8.44467
Average (Standard dev.)0.000394281 (±0.640937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-96
Dimensions384384192
Spacing384384192
CellA: 775.68 Å / B: 775.68 Å / C: 387.84 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.022.022.02
M x/y/z384384192
origin x/y/z0.0000.0000.000
length x/y/z775.680775.680387.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS-192-192-96
NC/NR/NS384384192
D min/max/mean-7.0648.4450.000

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Supplemental data

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Sample components

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Entire : Mature wild type bacteriophage lambda

EntireName: Mature wild type bacteriophage lambda
Components
  • Sample: Mature wild type bacteriophage lambda
  • Virus: Enterobacteria phage (virus)

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Supramolecule #1000: Mature wild type bacteriophage lambda

SupramoleculeName: Mature wild type bacteriophage lambda / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightExperimental: 20.9 MDa / Theoretical: 20.9 MDa

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Supramolecule #1: Enterobacteria phage

SupramoleculeName: Enterobacteria phage / type: virus / ID: 1 / Name.synonym: Bacteriophage lambda / Sci species name: Enterobacteria phage / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Bacteriophage lambda
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gpE / Diameter: 650 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

Concentration2 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-blotted for 7 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Side entry cryostage / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 78 K / Max: 78 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: objective lens astigmation corrected at 135,000 times magnification
DateSep 23, 2007
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 8058 / Average electron dose: 19 e/Å2 / Camera length: 61.4
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final two d classificationNumber classes: 1000
Final angle assignmentDetails: EMAN icos
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 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, then low-pass filtered.
Number images used: 31422
DetailsParticles selected using template-based selection, then manually checked. Particles were centered using EMAN cenalignint before reconstruction.

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Atomic model buiding 1

Initial modelPDB ID:

1c5e

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

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