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- EMDB-48226: cryoEM structure of Escherichia phage YDC107 tail core -

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Basic information

Entry
Database: EMDB / ID: EMD-48226
TitlecryoEM structure of Escherichia phage YDC107 tail core
Map data
Sample
  • Complex: Escherichia phage YDC107_1
    • Protein or peptide: Major tail protein V
Keywordsphage tail / bacteriophage / E. coli phage / YDC107 / helical tail / VIRUS / VIRAL PROTEIN
Function / homologyLambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Major tail protein V
Function and homology information
Biological speciesEscherichia phage YDC107_1 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsKopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Identification and cryoEM structure determination of Escherichia phage YDC107 tail found in a bacteria-contaminated buffer
Authors: Kopylov M / Jenkins MC
History
DepositionDec 9, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48226.png

Downloads & links

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Map

FileDownload / File: emd_48226.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å		1.06 Å/pix.
x 256 pix.
= 270.848 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.75001496 - 1.6343583
Average (Standard dev.)0.01147051 (±0.085175395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48226_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48226_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48226_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Escherichia phage YDC107_1

EntireName: Escherichia phage YDC107_1 (virus)
Components
  • Complex: Escherichia phage YDC107_1
    • Protein or peptide: Major tail protein V

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Supramolecule #1: Escherichia phage YDC107_1

SupramoleculeName: Escherichia phage YDC107_1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Tail fragments were identified in the contaminated buffer during cryoEM sample screening
Source (natural)Organism: Escherichia phage YDC107_1 (virus)

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Macromolecule #1: Major tail protein V

MacromoleculeName: Major tail protein V / type: protein_or_peptide / ID: 1
Details: Residues 155 and onwards are not resolved to high resolution and are excluded from the model
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage YDC107_1 (virus)
Molecular weightTheoretical: 25.699557 KDa
SequenceString: MPTPNPLPVK GAGTTLWVYK GNGDPYANPL SDVDWSRLAK VKDLTPGELT AESYDDSYLD DEDADWTATG QGQKSAGDTS FTLAWMPGE QGQQALLAWF NEGDTRAYKI RFPNGTVDVF RGWVSSIGKA VTAKEVITRT VKVTNVGRPS MAEDRSTVTA A TGMTVTPA ...String:
MPTPNPLPVK GAGTTLWVYK GNGDPYANPL SDVDWSRLAK VKDLTPGELT AESYDDSYLD DEDADWTATG QGQKSAGDTS FTLAWMPGE QGQQALLAWF NEGDTRAYKI RFPNGTVDVF RGWVSSIGKA VTAKEVITRT VKVTNVGRPS MAEDRSTVTA A TGMTVTPA SASVVKGQST TLTVAFQPEG ATDKSFRAVS SDKTKATVSV SGMTITVNGV AAGKVNIPVV SGNGEFAAVA EI TVTAS

UniProtKB: Major tail protein V

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 1 blot time 6.5 s.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 41.77 Å
Applied symmetry - Helical parameters - Δ&Phi: 17.90 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5927
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: Modelangelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9mfe:
cryoEM structure of Escherichia phage YDC107 tail core

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