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- EMDB-28039: Mycobacteriophage Muddy capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-28039
TitleMycobacteriophage Muddy capsid
Map dataSharpened map of Bayesian polished and ewald sphere corrected Muddy_postprocess.
Sample
  • Virus: Mycobacterium phage Muddy (virus)
    • Protein or peptide: Capsid
Function / homologyPhage capsid / Phage capsid family / Capsid
Function and homology information
Biological speciesMycobacterium phage Muddy (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFreeman KG / White SJ / Huet A / Conway JF
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131729 United States
Howard Hughes Medical Institute (HHMI)GT12053 United States
National Institutes of Health/Office of the DirectorOD019995 United States
National Institutes of Health/Office of the DirectorOD025009 United States
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 6, 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_28039.png

Downloads & links

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Map

FileDownload / File: emd_28039.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of Bayesian polished and ewald sphere corrected Muddy_postprocess.
Voxel sizeX=Y=Z: 1.076 Å
Density
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-15.437397 - 26.43991
Average (Standard dev.)1.2499024e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 860.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28039_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Ewald sphere corrected map of Muddy 3DRefine After Polishing And CTFRefine....

Fileemd_28039_additional_1.map
AnnotationEwald sphere corrected map of Muddy_3DRefine_After_Polishing_And_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 but after Bayesian...

Fileemd_28039_additional_2.map
AnnotationMap before ewald sphere correction but after Bayesian polishing and CTF Refinement.
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 Muddy 3DRefine After Polishing And CTFRefine.mrc....

Fileemd_28039_half_map_1.map
AnnotationHalf map of ewald sphere corrected Muddy_3DRefine_After_Polishing_And_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 Muddy 3DRefine After Polishing And CTFRefine.mrc....

Fileemd_28039_half_map_2.map
AnnotationHalf map of ewald sphere corrected Muddy_3DRefine_After_Polishing_And_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 : Mycobacterium phage Muddy

EntireName: Mycobacterium phage Muddy (virus)
Components
  • Virus: Mycobacterium phage Muddy (virus)
    • Protein or peptide: Capsid

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Supramolecule #1: Mycobacterium phage Muddy

SupramoleculeName: Mycobacterium phage Muddy / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Phage Muddy particles generated by amplification on bacterial host and purification via CsCl gradient.
NCBI-ID: 1340829 / Sci species name: Mycobacterium phage Muddy / 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: 710.0 Å / T number (triangulation number): 7

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Macromolecule #1: Capsid

MacromoleculeName: Capsid / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Muddy (virus)
Molecular weightTheoretical: 34.670102 KDa
SequenceString: AGFANIQGRA DLSDVHLPDQ VIKDVLQTAP EASVLLNRAR KVRMSSKKTK QPVLASLPDA YWVDGDTGLK QTTKNIWSNV FMTAEELAV IVPIPDALIA DSDLPLWDEV KPLLVEAIGK KVDDAGIFGN DKPASWPAAL IPGAIAAGNS VTLGTGDDIG V DVATLGEQ ...String:
AGFANIQGRA DLSDVHLPDQ VIKDVLQTAP EASVLLNRAR KVRMSSKKTK QPVLASLPDA YWVDGDTGLK QTTKNIWSNV FMTAEELAV IVPIPDALIA DSDLPLWDEV KPLLVEAIGK KVDDAGIFGN DKPASWPAAL IPGAIAAGNS VTLGTGDDIG V DVATLGEQ LALDGFSING FISRPGLHWS LVGLRNAQGQ PIYTPPLSTG LNGAPPTPAL YGFPLNEVTS GVWDADEAIL LG ADWSKVV IGIRQDITFD LFSEGVISDS DGKVVLNLMQ QDSKALRVVF RVGFQVANPM TRLNPNEATR YPAGVIIPAG GGS GEGEGE SE

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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
1.0 mMMgSO4Magnesium sulfate
68.44 mMNaClSodium chlorideSodium chloride
1.0 mMCaCl2Calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE-PROPANE / 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 opticsC2 aperture diameter: 50.0 µm / Illumination 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 / 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 / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1027 / Average exposure time: 40.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 28207
Startup modelType of model: INSILICO MODEL / Details: Relion SGD
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 25244
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-8edu:
Mycobacteriophage Muddy capsid

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