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- EMDB-22101: prohead of HK97 for packaging -

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Basic information

Entry
Database: EMDB / ID: EMD-22101
Titleprohead of HK97 for packaging
Map dataprohead of HK97 for packaging
Sample
  • Virus: Escherichia virus HK97
Function / homology: / Phage capsid / Phage capsid family / viral procapsid maturation / T=7 icosahedral viral capsid / viral capsid / identical protein binding / Major capsid protein
Function and homology information
Biological speciesEscherichia virus HK97
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 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: 10000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 10000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22101.png

Downloads & links

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Map

FileDownload / File: emd_22101.map.gz / Format: CCP4 / Size: 239.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationprohead of HK97 for packaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 501 pix.
= 686.37 Å		1.37 Å/pix.
x 501 pix.
= 686.37 Å		1.37 Å/pix.
x 501 pix.
= 686.37 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10000.0 / Movie #1: 10000
Minimum - Maximum-19462.0 - 32443.0
Average (Standard dev.)104.38888 (±3273.4185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions501501501
Spacing501501501
CellA=B=C: 686.37 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.371.371.37
M x/y/z501501501
origin x/y/z0.0000.0000.000
length x/y/z686.370686.370686.370
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS501501501
D min/max/mean-19462.00032443.000104.389

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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: 18306
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM / Number images used: 18306
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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