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- EMDB-69207: Cryo-EM structure of icosahedrally averaged bacteriophage RAN69 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-69207
TitleCryo-EM structure of icosahedrally averaged bacteriophage RAN69 capsid
Map data
Sample
  • Virus: Klebsiella phage RAN69 (virus)
    • Protein or peptide: decoration protein gp6
    • Protein or peptide: major capsid protein gp17
    • Protein or peptide: decoration protein gp5
Keywordsbacteriophage / RAN69 / capsid / VIRUS
Biological speciesKlebsiella phage RAN69 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRuan Z / Hu H / Wang A / Shao Q / Li X / Xie L / Sun Z / Yu J / Fang Q
Funding support China, 3 items
OrganizationGrant numberCountry
Other governmentJCYJ20250604174416022 China
Other governmentA2402025 China
National Natural Science Foundation of China (NSFC)32371285 China
CitationJournal: To Be Published
Title: Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome
Authors: Ruan Z / Hu H / Wang A / Shao Q / Li X / Xie L / Sun Z / Yu J / Fang Q
History
DepositionFeb 15, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69207.png

Downloads & links

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Map

FileDownload / File: emd_69207.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 600 pix.
= 899.64 Å		1.5 Å/pix.
x 600 pix.
= 899.64 Å		1.5 Å/pix.
x 600 pix.
= 899.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4994 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.070035346 - 0.12723929
Average (Standard dev.)0.0011601583 (±0.0073680896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 899.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69207_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69207_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_69207_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Klebsiella phage RAN69

EntireName: Klebsiella phage RAN69 (virus)
Components
  • Virus: Klebsiella phage RAN69 (virus)
    • Protein or peptide: decoration protein gp6
    • Protein or peptide: major capsid protein gp17
    • Protein or peptide: decoration protein gp5

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Supramolecule #1: Klebsiella phage RAN69

SupramoleculeName: Klebsiella phage RAN69 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3683496 / Sci species name: Klebsiella phage RAN69 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: decoration protein gp6

MacromoleculeName: decoration protein gp6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 12.978493 KDa
SequenceString:
MAAIIAAKTA DVQYAIVGTC QNLEKQVQPD YNVGFVGTTA LTKLNTFFTY MQSQGYTATR AGTAFKDDGT LQARLFSILS QLSKTGYVA LTGTGMPLGE GSGTAFDTSF TALQSAFVAA TDAAE

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Macromolecule #2: major capsid protein gp17

MacromoleculeName: major capsid protein gp17 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 37.696387 KDa
SequenceString: MADTIYKAGL TRPHWAGAQS DVDVHLEVYQ NEVDTRFQYQ ALFLGLSSQR SISGSNTYRI DRLNTSSVKG RRSGEALDST PVRNDKMII VVDTVLYIRN PIDYQDDWTG PDFLTEMGQN NGSEFAEVFD QAHLIQLIKG RSWVAPAHLK PAFNDGIEVG A AILVPGST ...String:
MADTIYKAGL TRPHWAGAQS DVDVHLEVYQ NEVDTRFQYQ ALFLGLSSQR SISGSNTYRI DRLNTSSVKG RRSGEALDST PVRNDKMII VVDTVLYIRN PIDYQDDWTG PDFLTEMGQN NGSEFAEVFD QAHLIQLIKG RSWVAPAHLK PAFNDGIEVG A AILVPGST SATQLTQAEM EANAMNINLA HKAGIDELIK RKTPLADMVT LVDVDTYSRL LEHPKLLNIE FGPSNNDGYK DR RVVKMNG VPVVECTEFP TAAGTHPLGS AYTVTSDDAL CRMVTFSKSK TLVTVEAKPF TSRIWDDERE FSNVLDCYAM YNI GLRRPD TAAVTKFTFT TKS

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Macromolecule #3: decoration protein gp5

MacromoleculeName: decoration protein gp5 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Molecular weightTheoretical: 6.172131 KDa
SequenceString:
MAIAKATSAQ QQELLRQLNI LGKALYAILT QPQNVAQTGA AFDTKIAALE AAVAAVKAAS

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 75628
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 7563
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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