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- EMDB-40077: Mycobacterium phage Patience -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-40077
TitleMycobacterium phage Patience
Map dataSharpened map of ewald sphere corrected postprocess.
Sample
  • Virus: Mycobacterium phage Patience (virus)
    • Protein or peptide: gp_4 (capsid accessory protein)
    • Protein or peptide: Capsid protein
    • Protein or peptide: gp_22 (Minor Capsid Protein)
KeywordsHK97-fold / T=7 / tailed bacteriophage / VIRUS
Function / homologyCapsid accessory protein / Minor capsid protein / Capsid protein
Function and homology information
Biological speciesMycobacterium phage Patience (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.39 Å
AuthorsPodgorski JM / White SJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A novel accessory protein stabilizes the capsid of two actinobacteriophages
Authors: Podgorski JM / Porgorski J / Gosselin S / Abad L / Jacobs-Sera D / Brown C / Hatfull G / Gogarten P / Luque A / White SJ
History
DepositionMar 14, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40077.png

Downloads & links

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Map

FileDownload / File: emd_40077.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of ewald sphere corrected postprocess.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.2 Å/pix.
x 800 pix.
= 960. Å		1.2 Å/pix.
x 800 pix.
= 960. Å		1.2 Å/pix.
x 800 pix.
= 960. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-9.725906999999999 - 18.055769000000002
Average (Standard dev.)0.000000000001212 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 960.00006 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Ewald sphere corrected map

Fileemd_40077_additional_1.map
AnnotationEwald sphere corrected 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_40077_additional_2.map
AnnotationMap after 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 Refine3D After CTFRefine.mrc.

Fileemd_40077_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_40077_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 : Mycobacterium phage Patience

EntireName: Mycobacterium phage Patience (virus)
Components
  • Virus: Mycobacterium phage Patience (virus)
    • Protein or peptide: gp_4 (capsid accessory protein)
    • Protein or peptide: Capsid protein
    • Protein or peptide: gp_22 (Minor Capsid Protein)

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Supramolecule #1: Mycobacterium phage Patience

SupramoleculeName: Mycobacterium phage Patience / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1074308 / Sci species name: Mycobacterium phage Patience / 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): 7

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Macromolecule #1: gp_4 (capsid accessory protein)

MacromoleculeName: gp_4 (capsid accessory protein) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Patience (virus)
Molecular weightTheoretical: 10.549938 KDa
SequenceString:
MANRTVSPST QGVRPAMRQM YNGRNVATRP IPLIVDTSEI RAIMAAAADA RPKTSAVNFP QSGPRPAGAA VVFGTKVSGA PGNVVSNNA ATFAPLTGTQ NFE

UniProtKB: Capsid accessory protein

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Macromolecule #2: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Patience (virus)
Molecular weightTheoretical: 43.845391 KDa
SequenceString: MATKELKIGG VPVFPIFGGT APVRQEGIMT QGDLVTVTSD GIDLNALWNS FAESIAIYNE AMDNLIQLLT YPVTVPVEPV VQIGETTFE EATELGVPRG AGLPIEVFQM GYDLRHYDKR NAYSWMFLAD ADGRQVEAIH DAVLWADKRL VFRKVMEALF D NRTRRANI ...String:
MATKELKIGG VPVFPIFGGT APVRQEGIMT QGDLVTVTSD GIDLNALWNS FAESIAIYNE AMDNLIQLLT YPVTVPVEPV VQIGETTFE EATELGVPRG AGLPIEVFQM GYDLRHYDKR NAYSWMFLAD ADGRQVEAIH DAVLWADKRL VFRKVMEALF D NRTRRANI RNQAYNVYPL YNGDGVPPPR FKNNVFDETH SHYVISHNSV VDSSDLEDLM ELLAEHGYSP QAGTQFLLLA NK AETDAIR QFRRGVVNNN GATAGYDFIP SPTQPAMMLP NAEGLLGNQP APTFGGLAVI GSYGFWNIVE EDYIPPGYLV GVG YGGAFN LGNPVGLRQH ANPAMQGLRI IAGNYQRYPL VDGFYARSFG TGVRQRGGAA IMQIKASGAY ECPPIYKKGG GFLV

UniProtKB: Capsid protein

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Macromolecule #3: gp_22 (Minor Capsid Protein)

MacromoleculeName: gp_22 (Minor Capsid Protein) / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Patience (virus)
Molecular weightTheoretical: 23.845107 KDa
SequenceString: MALKTKPRWD KYDGYVGNYR GVLGEDIDLD TEANRVLAVG TNSNGAIVVG AGQTGIKGLM IVAVGADIHG AMLDGGINNH AGDPQDVGK HGEITNFQPT VFGRTFGVAI SATEGNVKLA VNGVDTGNIA YDTSAANLKS GIVAVDDGFT ADDFTVTGTA P NFTIVTTR ...String:
MALKTKPRWD KYDGYVGNYR GVLGEDIDLD TEANRVLAVG TNSNGAIVVG AGQTGIKGLM IVAVGADIHG AMLDGGINNH AGDPQDVGK HGEITNFQPT VFGRTFGVAI SATEGNVKLA VNGVDTGNIA YDTSAANLKS GIVAVDDGFT ADDFTVTGTA P NFTIVTTR TDVTITASGE GVTVTEATSV AAAGTNYYGH ADGTVNAVKG SDGVYVGHTQ EADRLIVNVK DEED

UniProtKB: Minor 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: 8640 / Average electron dose: 30.0 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) / Resolution.type: BY AUTHOR / Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 61957
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-8giu:
Mycobacterium phage Patience

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