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- EMDB-29390: Prohead I ico symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-29390
TitleProhead I ico symmetry
Map dataicosahedral symmetry
Sample
  • Virus: Escherichia phage HK97 (virus)
    • Protein or peptide: Scaffolding domain delta
KeywordsProhead I / icosahedral symmetry / HK97 / phage / capsid / VIRUS
Function / homologyPhage 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 phage HK97 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 28, 2023-
Current statusJun 28, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29390.png

Downloads & links

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Map

FileDownload / File: emd_29390.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationicosahedral symmetry
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.053927187 - 0.1100935
Average (Standard dev.)0.000021029573 (±0.005235879)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-349-349-349
Dimensions700700700
Spacing700700700
CellA=B=C: 756.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29390_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_29390_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: Scaffolding domain delta

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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: Scaffolding domain delta

MacromoleculeName: Scaffolding domain delta / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage HK97 (virus)
Molecular weightTheoretical: 42.286453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSELALIQKA IEESQQKMTQ LFDAQKAEIE STGQVSKQLQ SDLMKVQEEL TKSGTRLFDL EQKLASGAEN PGEKKSFSER AAEELIKSW DGKQGTFGAK TFNKSLGSDA DSAGSLIQPM QIPGIIMPGL RRLTIRDLLA QGRTSSNALE YVREEVFTNN A DVVAEKAL ...String:
MSELALIQKA IEESQQKMTQ LFDAQKAEIE STGQVSKQLQ SDLMKVQEEL TKSGTRLFDL EQKLASGAEN PGEKKSFSER AAEELIKSW DGKQGTFGAK TFNKSLGSDA DSAGSLIQPM QIPGIIMPGL RRLTIRDLLA QGRTSSNALE YVREEVFTNN A DVVAEKAL KPESDITFSK QTANVKTIAH WVQASRQVMD DAPMLQSYIN NRLMYGLALK EEGQLLNGDG TGDNLEGLNK VA TAYDTSL NATGDTRADI IAHAIYQVTE SEFSASGIVL NPRDWHNIAL LKDNEGRYIF GGPQAFTSNI MWGLPVVPTK AQA AGTFTV GGFDMASQVW DRMDATVEVS REDRDNFVKN MLTILCEERL ALAHYRPTAI IKGTFSSGS

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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 ChlorideNaClSodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
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
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 FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 72945
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8fqk:
Asymmetric unit of HK97 phage prohead I

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