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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: Structure / Year: 2026
Title: Near-complete cryo-EM structure of the Klebsiella pneumoniae podophage RAN69 reveals tail fiber-spike interface and a divergent pre-ejectosome.
Authors: Zhiyang Ruan / Hongli Hu / Aohan Wang / Qianqian Shao / Xiangyun Li / Linlin Xie / Zhuo Sun / Jiaxin Yu / Qianglin Fang /
Abstract: Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures ...Carbapenem-resistant Klebsiella pneumoniae is a critical-priority pathogen, underscoring the need for alternatives to antibiotics. Bacteriophages are promising agents, yet high-resolution structures of K. pneumoniae phages are scarce. Here, we report near-complete cryo-electron microscopic reconstructions of the K. pneumoniae podophage RAN69 at 3.0-3.4 Å resolution, enabling atomic models for 12 structural components. Complete in situ structures of the long tail fiber (gp9 trimer) and distal tail spike (gp1 trimer) are resolved, revealing a previously unknown binding interface in which the gp1 N-terminal arm wedges between spike-binding domains of gp9. The pre-ejectosome forms a conserved double-layered assembly (gp10 tetramer over gp11 octamer), tethered to the portal by an octameric gp12 that inserts long helices into the portal barrel, with gp20 reinforcing gp11 interfaces. Divergent folds in gp10 and a lysozyme-like gp11 peripheral domain suggest adaptation to host envelopes. These structures advance our understanding of podophage assembly.
History
DepositionFeb 15, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 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
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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

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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
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Half map: #2

Fileemd_69207_half_map_1.map
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Half map: #1

Fileemd_69207_half_map_2.map
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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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