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- EMDB-22100: Hk97 prohead during packaging (sym6) -

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Basic information

Entry
Database: EMDB / ID: EMD-22100
TitleHk97 prohead during packaging (sym6)
Map dataHk97 prohead during packaging (sym6)
Sample
  • Virus: Escherichia virus HK97
Function / homology
Function and homology information


viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding
Similarity search - Function
Terminase large subunit-like / Terminase large subunit, ATPase domain / Phage capsid / Phage capsid family
Similarity search - Domain/homology
Major capsid protein / Terminase small subunit / Terminase large subunit
Similarity search - Component
Biological speciesEscherichia virus HK97
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsFung HKH / Grimes S / Huet A / Duda RLD / Chechick M / Gault J / Robinson CV / Jardine PJ / Conway JF / Baumann CG / Antson AA
Funding support United Kingdom, United States, 4 items
OrganizationGrant numberCountry
Wellcome Trust098230 United Kingdom
Wellcome Trust095024MA United Kingdom
National Institutes of Health/National Library of Medicine (NIH/NLM)S10OD019995 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)R01GM047795 United States
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system.
Authors: Herman K H Fung / Shelley Grimes / Alexis Huet / Robert L Duda / Maria Chechik / Joseph Gault / Carol V Robinson / Roger W Hendrix / Paul J Jardine / James F Conway / Christoph G Baumann / Alfred A Antson /
Abstract: Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and ...Many essential cellular processes rely on substrate rotation or translocation by a multi-subunit, ring-type NTPase. A large number of double-stranded DNA viruses, including tailed bacteriophages and herpes viruses, use a homomeric ring ATPase to processively translocate viral genomic DNA into procapsids during assembly. Our current understanding of viral DNA packaging comes from three archetypal bacteriophage systems: cos, pac and phi29. Detailed mechanistic understanding exists for pac and phi29, but not for cos. Here, we reconstituted in vitro a cos packaging system based on bacteriophage HK97 and provided a detailed biochemical and structural description. We used a photobleaching-based, single-molecule assay to determine the stoichiometry of the DNA-translocating ATPase large terminase. Crystal structures of the large terminase and DNA-recruiting small terminase, a first for a biochemically defined cos system, reveal mechanistic similarities between cos and pac systems. At the same time, mutational and biochemical analyses indicate a new regulatory mechanism for ATPase multimerization and coordination in the HK97 system. This work therefore establishes a framework for studying the evolutionary relationships between ATP-dependent DNA translocation machineries in double-stranded DNA viruses.
History
DepositionJun 2, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6000
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22100.png

Downloads & links

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Map

FileDownload / File: emd_22100.map.gz / Format: CCP4 / Size: 48.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHk97 prohead during packaging (sym6)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.11 Å/pix.
x 233 pix.
= 957.63 Å		4.11 Å/pix.
x 233 pix.
= 957.63 Å		4.11 Å/pix.
x 233 pix.
= 957.63 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6000.0 / Movie #1: 6000
Minimum - Maximum-11533.75 - 30936.309
Average (Standard dev.)248.62029 (±3264.0745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-116-116-116
Dimensions233233233
Spacing233233233
CellA=B=C: 957.63 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.114.114.11
M x/y/z233233233
origin x/y/z0.0000.0000.000
length x/y/z957.630957.630957.630
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-116-116-116
NC/NR/NS233233233
D min/max/mean-11533.75030936.309248.620

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Supplemental data

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Sample components

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Entire : Escherichia virus HK97

EntireName: Escherichia virus HK97
Components
  • Virus: Escherichia virus HK97

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Supramolecule #1: Escherichia virus HK97

SupramoleculeName: Escherichia virus HK97 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 37554 / Sci species name: Escherichia virus HK97 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: escher (unknown)
Molecular weightTheoretical: 13 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 350.0 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: 8
Component:
ConcentrationNameFormula
20.0 mMtris
10.0 mMMgSo4
30.0 mMPotassium glutamate
1.0 mMbeta mercaptoethanol
1.0 mMAtp
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II / Details: 8 sec blot.

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 971 / Average exposure time: 1.65 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 78000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 866
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM / Number images used: 866
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final angle assignmentType: COMMON LINE

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