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- EMDB-27824: Mycobacterium phage Che8 -

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Basic information

Entry
Database: EMDB / ID: EMD-27824
TitleMycobacterium phage Che8
Map dataSharpened map of Ewald sphere corrected Che8_postprocess
Sample
  • Virus: Mycobacterium phage Che8 (virus)
    • Protein or peptide: Major capsid protein, gp6
KeywordsHK97-fold / T=9 / tailed bacteriophage / VIRUS
Function / homologyMajor capsid protein
Function and homology information
Biological speciesMycobacterium virus Che8 / Mycobacterium phage Che8 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPodgorski JM / White SJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: A structural dendrogram of the actinobacteriophage major capsid proteins provides important structural insights into the evolution of capsid stability.
Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten ...Authors: Jennifer M Podgorski / Krista Freeman / Sophia Gosselin / Alexis Huet / James F Conway / Mary Bird / John Grecco / Shreya Patel / Deborah Jacobs-Sera / Graham Hatfull / Johann Peter Gogarten / Janne Ravantti / Simon J White /
Abstract: Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. ...Many double-stranded DNA viruses, including tailed bacteriophages (phages) and herpesviruses, use the HK97-fold in their major capsid protein to make the capsomers of the icosahedral viral capsid. After the genome packaging at near-crystalline densities, the capsid is subjected to a major expansion and stabilization step that allows it to withstand environmental stresses and internal high pressure. Several different mechanisms for stabilizing the capsid have been structurally characterized, but how these mechanisms have evolved is still not understood. Using cryo-EM structure determination of 10 capsids, structural comparisons, phylogenetic analyses, and Alphafold predictions, we have constructed a detailed structural dendrogram describing the evolution of capsid structural stability within the actinobacteriophages. We show that the actinobacteriophage major capsid proteins can be classified into 15 groups based upon their HK97-fold.
History
DepositionAug 9, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27824.png

Downloads & links

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Map

FileDownload / File: emd_27824.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Ewald sphere corrected Che8_postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 800 pix.
= 849.92 Å		1.06 Å/pix.
x 800 pix.
= 849.92 Å		1.06 Å/pix.
x 800 pix.
= 849.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0624 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-9.0420885 - 20.886133000000001
Average (Standard dev.)0.000000000000217 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 849.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ewald sphere corrected map of 3DRefine After CTFRefine

Fileemd_27824_additional_1.map
AnnotationEwald sphere corrected map of 3DRefine_After_CTFRefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map before Ewald sphere correction

Fileemd_27824_additional_2.map
AnnotationMap before Ewald sphere correction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Ewald sphere corrected 3DRefine After CTFRefine

Fileemd_27824_half_map_1.map
AnnotationHalf map of Ewald sphere corrected 3DRefine_After_CTFRefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of Ewald sphere corrected 3DRefine After CTFRefine

Fileemd_27824_half_map_2.map
AnnotationHalf map of Ewald sphere corrected 3DRefine_After_CTFRefine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium phage Che8

EntireName: Mycobacterium phage Che8 (virus)
Components
  • Virus: Mycobacterium phage Che8 (virus)
    • Protein or peptide: Major capsid protein, gp6

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Supramolecule #1: Mycobacterium phage Che8

SupramoleculeName: Mycobacterium phage Che8 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2907829 / Sci species name: Mycobacterium phage Che8 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Virus shellShell ID: 1 / Diameter: 730.0 Å / T number (triangulation number): 9

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Macromolecule #1: Major capsid protein, gp6

MacromoleculeName: Major capsid protein, gp6 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium virus Che8
Molecular weightTheoretical: 29.075291 KDa
SequenceString: MAFNNFIPEL WSDMLLEEWT AQTVFANLVN REYEGIASKG NVVHIAGVVA PTVKDYKAAG RQTSADAISD TGVDLLIDQE KSIDFLVDD IDRVQVAGSL EAYTRAGATA LATDTDKFIA DMLVDNGTAL TGSAPSDADD AFDLIASALK ELTKANVPNV G RVVVVNAE ...String:
MAFNNFIPEL WSDMLLEEWT AQTVFANLVN REYEGIASKG NVVHIAGVVA PTVKDYKAAG RQTSADAISD TGVDLLIDQE KSIDFLVDD IDRVQVAGSL EAYTRAGATA LATDTDKFIA DMLVDNGTAL TGSAPSDADD AFDLIASALK ELTKANVPNV G RVVVVNAE MAFWLRSSGS KLTSADTSGD AAGLRAGTIG NLLGARIVES NNLRDTDDEQ FVAFHPSAAA YVSQIDTVEA LR DQDSFSD RIRALHVYGG KVVRPTGVVV FNKTGS

UniProtKB: Major capsid 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:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
10.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chloride
GridModel: C-flat-2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 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 real images: 1201 / Average electron dose: 1.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / Details: Relion SGD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 14972
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.0)

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Atomic model buiding 1

DetailsAmino acid sequence built into the map for a single major capsid protein and refined with Phenix. Model then used for rest of asymmetric unit and refined with Phenix. Final step involved using Isolde.
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8e16:
Mycobacterium phage Che8

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