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- EMDB-28017: Mycobacterium phage Cain -

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Basic information

Entry
Database: EMDB / ID: EMD-28017
TitleMycobacterium phage Cain
Map dataSharpened map of ewald sphere corrected map.
Sample
  • Virus: Mycobacterium phage Cain (virus)
    • Protein or peptide: Major capsid protein
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Cain (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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
DepositionSep 2, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_28017.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected map.
Voxel sizeX=Y=Z: 1.2024 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-10.247826 - 22.472641
Average (Standard dev.)9.381728e-13 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 961.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28017_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Ewald sphere corrected map.

Fileemd_28017_additional_1.map
AnnotationEwald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Map before CTF refinement

Fileemd_28017_additional_2.map
AnnotationMap before CTF refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of ewald sphere corrected map.

Fileemd_28017_half_map_1.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map of ewald sphere corrected map.

Fileemd_28017_half_map_2.map
AnnotationHalf map of ewald sphere corrected map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Mycobacterium phage Cain

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

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Supramolecule #1: Mycobacterium phage Cain

SupramoleculeName: Mycobacterium phage Cain / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2015818 / Sci species name: Mycobacterium phage Cain / 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: 750.0 Å / T number (triangulation number): 9

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Cain (virus)
Molecular weightTheoretical: 31.892002 KDa
SequenceString: MADISRAEVA TLIQEAYSDT LLAAAKQGST VLSAFQNVNM GTKTTHLPVL ATLPEAGWVG ESATEPEGVI PTSKVTWANR TLVAEEVAV IIPVPEAVID DATVAILTEV AEQGGQAIGK KLDQAVIFGI DKPASWVSPA LVPAAVAAGQ AIAHVSGVAN E FDLVGASN ...String:
MADISRAEVA TLIQEAYSDT LLAAAKQGST VLSAFQNVNM GTKTTHLPVL ATLPEAGWVG ESATEPEGVI PTSKVTWANR TLVAEEVAV IIPVPEAVID DATVAILTEV AEQGGQAIGK KLDQAVIFGI DKPASWVSPA LVPAAVAAGQ AIAHVSGVAN E FDLVGASN KVAEKVALAG WAPDTLLSSL ALRYQVANVR DADGNLAFRD GSFLGFNTHF NRNGAWAPTS AVGVIADSSR VK IGVRQDI TVKFLDQATL GTGENQINLA ERDMVALRLK ARFAYVLGVS ATSVGANQTP VGVVTPDVTA

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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 chlorideSodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 4368 / Average electron dose: 0.83 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / Details: Relion SGD
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 31878
FSC plot (resolution estimation)

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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-8ecj:
Mycobacterium phage Cain

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