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- EMDB-29392: portal vertex of HK97 phage -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29392
Titleportal vertex of HK97 phage
Map data
Sample
  • Virus: Escherichia phage HK97 (virus)
    • Protein or peptide: Portal protein
KeywordsProhead I / icosahedral symmetry / HK97 / phage / capsid / VIRUS
Function / homologyPhage portal protein, HK97 / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral capsid / Portal protein
Function and homology information
Biological speciesEscherichia phage HK97 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHuet A / Oh B / Maurer J / Duda RL / Conway JF
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM144981 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM47795 United States
CitationJournal: Sci Adv / Year: 2023
Title: A symmetry mismatch unraveled: How phage HK97 scaffold flexibly accommodates a 12-fold pore at a 5-fold viral capsid vertex.
Authors: Alexis Huet / Bonnie Oh / Josh Maurer / Robert L Duda / James F Conway /
Abstract: Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold ...Tailed bacteriophages and herpesviruses use a transient scaffold to assemble icosahedral capsids with hexameric capsomers on the faces and pentameric capsomers at all but one vertex where a 12-fold portal is thought to nucleate the assembly. How does the scaffold orchestrate this step? We have determined the portal vertex structure of the bacteriophage HK97 procapsid, where the scaffold is a domain of the major capsid protein. The scaffold forms rigid helix-turn-strand structures on the interior surfaces of all capsomers and is further stabilized around the portal, forming trimeric coiled-coil towers, two per surrounding capsomer. These 10 towers bind identically to 10 of 12 portal subunits, adopting a pseudo-12-fold organization that explains how the symmetry mismatch is managed at this early step.
History
DepositionJan 6, 2023-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29392.png

Downloads & links

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Map

FileDownload / File: emd_29392.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07039683 - 0.121377304
Average (Standard dev.)0.000117523574 (±0.0072959745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29392_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_29392_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Escherichia phage HK97

EntireName: Escherichia phage HK97 (virus)
Components
  • Virus: Escherichia phage HK97 (virus)
    • Protein or peptide: Portal protein

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Supramolecule #1: Escherichia phage HK97

SupramoleculeName: Escherichia phage HK97 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Prohead I expressed from plasmid in E.Coli / NCBI-ID: 2681617 / Sci species name: Escherichia phage HK97 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 17.7 MDa
Virus shellShell ID: 1 / Name: Prohead I / Diameter: 500.0 Å / T number (triangulation number): 7

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage HK97 (virus)
Molecular weightTheoretical: 47.318488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDN RKKVDLSNPL ARLLRYSPNQ YMTAQEFREA MTMQLCFYGN AYALVDRNSA GDVISLLPLQ SANMDVKLVG K KVVYRYQR ...String:
MEEPKYTIDL RTNNGWWARL KSWFVGGRLV TPNQGSQTGP VSAHGYLGDS SINDERILQI STVWRCVSLI STLTACLPLD VFETDQNDN RKKVDLSNPL ARLLRYSPNQ YMTAQEFREA MTMQLCFYGN AYALVDRNSA GDVISLLPLQ SANMDVKLVG K KVVYRYQR DSEYADFSQK EIFHLKGFGF TGLVGLSPIA FACKSAGVAV AMEDQQRDFF ANGAKSPQIL STGEKVLTEQ QR SQVEENF KEIAGGPVKK RLWILEAGFS TSAIGVTPQD AEMMASRKFQ VSELARFFGV PPHLVGDVEK STSWGSGIEQ QNL GFLQYT LQPYISRWEN SIQRWLIPSK DVGRLHAEHN LDGLLRGDSA SRAAFMKAMG ESGLRTINEM RRTDNMPPLP GGDV AMRQA QYVPITDLGT NKEPRNNGA

UniProtKB: Portal protein

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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

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMtris
100.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2909 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 4.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 72945
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8fql:
Portal vertex of HK97 phage

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