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- EMDB-27992: Gordonia phage Ziko -

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Basic information

Entry
Database: EMDB / ID: EMD-27992
TitleGordonia phage Ziko
Map dataSharpened map of ewald sphere corrected postprocess_ewald.
Sample
  • Virus: Gordonia phage Ziko (virus)
    • Protein or peptide: Major capsid protein
Function / homologyPhage capsid / Phage capsid family / Major capsid protein
Function and homology information
Biological speciesGordonia phage Ziko (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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 30, 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

emd_27992.png

Downloads & links

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Map

FileDownload / File: emd_27992.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected postprocess_ewald.
Voxel sizeX=Y=Z: 1.28256 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-10.89247 - 20.98067
Average (Standard dev.)-1.559086e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 961.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27992_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map after CTF Refinement.

Fileemd_27992_additional_1.map
AnnotationMap after CTF Refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map before CTF Refinement.

Fileemd_27992_additional_2.map
AnnotationMap before CTF Refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ewald sphere corrected map of Refine3D After CTFRefine.

Fileemd_27992_additional_3.map
AnnotationEwald sphere corrected map of Refine3D_After_CTFRefine.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map of ewald sphere corrected Refine3D After CTFRefine.mrc.

Fileemd_27992_half_map_1.map
AnnotationHalf map of ewald sphere corrected Refine3D_After_CTFRefine.mrc.
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 Refine3D After CTFRefine.mrc.

Fileemd_27992_half_map_2.map
AnnotationHalf map of ewald sphere corrected Refine3D_After_CTFRefine.mrc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gordonia phage Ziko

EntireName: Gordonia phage Ziko (virus)
Components
  • Virus: Gordonia phage Ziko (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Gordonia phage Ziko

SupramoleculeName: Gordonia phage Ziko / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2591193 / Sci species name: Gordonia phage Ziko / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Gordonia terrae (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: Gordonia phage Ziko (virus)
Molecular weightTheoretical: 34.203129 KDa
SequenceString: MADTNRTDAA ALIQEAYSDV FLDSVSETAK VIGTFPVYNM GTKTTNLPVL STFPHAKWVG ESATAPEGVK PTAKATWANK TLVAEELAV ILPIHENVLA DATEDLLAEL ARMGGASIGR ALDAAVLFGH QKPVTWASKS LFESADDAGQ VVAVGNSNGV E GDDISGSI ...String:
MADTNRTDAA ALIQEAYSDV FLDSVSETAK VIGTFPVYNM GTKTTNLPVL STFPHAKWVG ESATAPEGVK PTAKATWANK TLVAEELAV ILPIHENVLA DATEDLLAEL ARMGGASIGR ALDAAVLFGH QKPVTWASKS LFESADDAGQ VVAVGNSNGV E GDDISGSI LQAAEMVADV YDPSHLLGYS GLRYRLANQR DANGQPLFQP YMQGTPGSDG MVHGLNTVFF SGNVDDGSNG DA PVWDRDV ASAIVVDRSR VVIGVRQDIT VKYLDQATVG GINLAERDMV ALRFCGRFAY ALGDNIAQGR VAAENSPVAV ITP YAGS

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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: 3.0 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: 5058 / Average electron dose: 0.87 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 reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 35950

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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-8eb4:
Gordonia phage Ziko

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