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- EMDB-28012: Mycobacterium phage Adephagia -

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Basic information

Entry
Database: EMDB / ID: EMD-28012
TitleMycobacterium phage Adephagia
Map dataSharpened map of ewald sphere corrected Adephagia_Ewald_postprocess.
Sample
  • Virus: Mycobacterium phage Adephagia (virus)
    • Protein or peptide: Major capsid protein
KeywordsHK97-fold / T=9 / tailed bacteriophage / VIRUS
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesMycobacterium phage Adephagia (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 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 1, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28012.png

Downloads & links

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Map

FileDownload / File: emd_28012.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected Adephagia_Ewald_postprocess.
Projections & slices

Image control

Size
Brightness
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Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.2 Å/pix.
x 800 pix.
= 961.92 Å		1.2 Å/pix.
x 800 pix.
= 961.92 Å		1.2 Å/pix.
x 800 pix.
= 961.92 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-11.701378 - 23.174398
Average (Standard dev.)0.000000000001103 (±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_28012_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Ewald sphere corrected map of Adephagia Refine3D AfterCTFRefine run class001....

Fileemd_28012_additional_1.map
AnnotationEwald sphere corrected map of Adephagia_Refine3D_AfterCTFRefine_run_class001.
Projections & Slices
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Additional map: Map before ewald sphere correction.

Fileemd_28012_additional_2.map
AnnotationMap before ewald sphere correction.
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Additional map: Map before CTF Refinement

Fileemd_28012_additional_3.map
AnnotationMap before CTF Refinement
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Half map: Half map of ewald sphere corrected Adephagia Refine3D AfterCTFRefine run class001....

Fileemd_28012_half_map_1.map
AnnotationHalf map of ewald sphere corrected Adephagia_Refine3D_AfterCTFRefine_run_class001.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected Adephagia Refine3D AfterCTFRefine run class001....

Fileemd_28012_half_map_2.map
AnnotationHalf map of ewald sphere corrected Adephagia_Refine3D_AfterCTFRefine_run_class001.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Sample components

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Entire : Mycobacterium phage Adephagia

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

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Supramolecule #1: Mycobacterium phage Adephagia

SupramoleculeName: Mycobacterium phage Adephagia / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2907829 / Sci species name: Mycobacterium phage Adephagia / 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: 760.0 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 Adephagia (virus)
Molecular weightTheoretical: 32.753832 KDa
SequenceString: MADISRAEVA TLIEEGYSHS LLAAAKQGST VLSAFQNVNM GTKTTHLPVL ATLPEADWVG ESATDPEGVI KTSKVTWANR TLVAEEVAV IIPVPEAVID DATVELLTEV AEQGGQAIGK KLDQAVMFGI DKPASWVSPA LLKAATDAGQ AIAHVSGVAN E YDLVGASN ...String:
MADISRAEVA TLIEEGYSHS LLAAAKQGST VLSAFQNVNM GTKTTHLPVL ATLPEADWVG ESATDPEGVI KTSKVTWANR TLVAEEVAV IIPVPEAVID DATVELLTEV AEQGGQAIGK KLDQAVMFGI DKPASWVSPA LLKAATDAGQ AIAHVSGVAN E YDLVGASN KVAEQVALAG WAPDTLLSSL ALRYQVANVR DADGNLAFRD GSFLGFNTHF NRNGAWSPES AVAFIADSSR VK IGVRQDI TVKFLDQATL GTGDNQINLA ERDMVALRLK ARFAYVLGVS ATAMGANKTP VGVVTPDVTP PTSGE

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
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: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 5688 / Average electron dose: 0.48 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 51783
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)
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-8ec2:
Mycobacterium phage Adephagia

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