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- EMDB-5829: Architecture of a dsDNA viral capsid in complex with its maturati... -

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Entry
Database: EMDB / ID: EMD-5829
TitleArchitecture of a dsDNA viral capsid in complex with its maturation protease
Map dataProhead-1 with protease (before sharpening). A negative temperature factor of -300 A2 or -700 A2 should be applied to better visualize the features of the scaffolding domains or the coat subunit shell, respectively.
Sample
  • Sample: HK97 Prohead-1 with protease
  • Virus: Enterobacteria phage HK97 (virus)
KeywordsBacteriophage HK97 / virus maturation / electron cryo-microscopy / scaffolding proteins
Biological speciesEnterobacteria phage HK97 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsVeesler D / Khayat R / Krishnamurthy S / Snijder J / Huang RK / Heck AJR / Anand GS / Johnson JE
CitationJournal: Structure / Year: 2014
Title: Architecture of a dsDNA viral capsid in complex with its maturation protease.
Authors: David Veesler / Reza Khayat / Srinath Krishnamurthy / Joost Snijder / Rick K Huang / Albert J R Heck / Ganesh S Anand / John E Johnson /
Abstract: Most double-stranded DNA (dsDNA) viruses, including bacteriophages and herpesviruses, rely on a staged assembly process of capsid formation. A viral protease is required for many of them to ...Most double-stranded DNA (dsDNA) viruses, including bacteriophages and herpesviruses, rely on a staged assembly process of capsid formation. A viral protease is required for many of them to disconnect scaffolding domains/proteins from the capsid shell, therefore priming the maturation process. We used the bacteriophage HK97 as a model system to decipher the molecular mechanisms underlying the recruitment of the maturation protease by the assembling procapsid and the influence exerted onto the latter. Comparisons of the procapsid with and without protease using single-particle cryoelectron microscopy reconstructions, hydrogen/deuterium exchange coupled to mass spectrometry, and native mass spectrometry demonstrated that the protease interacts with the scaffolding domains within the procapsid interior and stabilizes them as well as the whole particle. The results suggest that the thermodynamic consequences of protease packaging are to shift the equilibrium between isolated coat subunit capsomers and procapsid in favor of the latter by stabilizing the assembled particle before making the process irreversible through proteolysis of the scaffolding domains.
History
DepositionDec 2, 2013-
Header (metadata) releaseMar 19, 2014-
Map releaseMar 19, 2014-
UpdateMar 19, 2014-
Current statusMar 19, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_5829.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProhead-1 with protease (before sharpening). A negative temperature factor of -300 A2 or -700 A2 should be applied to better visualize the features of the scaffolding domains or the coat subunit shell, respectively.
Voxel sizeX=Y=Z: 2.75 Å
Density
Contour LevelBy EMDB: 0.0826 / Movie #1: 0.01
Minimum - Maximum-0.05285095 - 0.16055299
Average (Standard dev.)-0.03716557 (±0.01885428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 1188.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.752.752.75
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z1188.0001188.0001188.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0530.161-0.037

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Supplemental data

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Sample components

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Entire : HK97 Prohead-1 with protease

EntireName: HK97 Prohead-1 with protease
Components
  • Sample: HK97 Prohead-1 with protease
  • Virus: Enterobacteria phage HK97 (virus)

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Supramolecule #1000: HK97 Prohead-1 with protease

SupramoleculeName: HK97 Prohead-1 with protease / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1

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Supramolecule #1: Enterobacteria phage HK97

SupramoleculeName: Enterobacteria phage HK97 / type: virus / ID: 1 / NCBI-ID: 37554 / Sci species name: Enterobacteria phage HK97 / Sci species strain: HK97 / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: gp5 / Diameter: 540 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

BufferpH: 7.5 / Details: 10 mM Tris, 40 mM monosodium glutamate
GridDetails: C-flat
VitrificationCryogen name: ETHANE / Chamber temperature: 94 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 109489 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.157 µm / Nominal defocus min: 0.818 µm
Sample stageSpecimen holder: Liquid Nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 90 K
DateJan 7, 2009
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 152 / Average electron dose: 16 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: OTHER / Software - Name: Frealign / Details: Resolution-limited refinement to 10 A / Number images used: 2970

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