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- PDB-23sg: The composite Cryo-EM structure of bacteriophage RAN69 pre-ejecto... -

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Basic information

Entry
Database: PDB / ID: 23sg
TitleThe composite Cryo-EM structure of bacteriophage RAN69 pre-ejectosome-portal complex
Components
  • gp10
  • gp11
  • gp12
  • gp20
  • portal gp19
KeywordsVIRUS / bacteriophage / RAN69 / pre-ejectosome-portal complex
Biological speciesKlebsiella phage RAN69 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsRuan, Z. / Hu, H. / Wang, A. / Shao, Q. / Li, X. / Xie, L. / Sun, Z. / Yu, J. / Fang, Q.
Funding support China, 3items
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 2.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: gp11
X: gp12
a: gp12
S: gp10
G: gp11
d: portal gp19
A: portal gp19
D: portal gp19
m: gp20
g: gp20


Theoretical massNumber of molelcules
Total (without water)562,96410
Polymers562,96410
Non-polymers00
Water00
1
N: gp11
X: gp12
a: gp12
S: gp10
G: gp11
d: portal gp19
A: portal gp19
D: portal gp19
m: gp20
g: gp20

N: gp11
X: gp12
a: gp12
S: gp10
G: gp11
d: portal gp19
A: portal gp19
D: portal gp19
m: gp20
g: gp20

N: gp11
X: gp12
a: gp12
S: gp10
G: gp11
d: portal gp19
A: portal gp19
D: portal gp19
m: gp20
g: gp20

N: gp11
X: gp12
a: gp12
S: gp10
G: gp11
d: portal gp19
A: portal gp19
D: portal gp19
m: gp20
g: gp20


Theoretical massNumber of molelcules
Total (without water)2,251,85440
Polymers2,251,85440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3

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Components

#1: Protein gp11


Mass: 96890.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#2: Protein gp12


Mass: 20921.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#3: Protein gp10


Mass: 135202.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#4: Protein portal gp19


Mass: 58217.703 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#5: Protein gp20


Mass: 8741.618 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Klebsiella phage RAN69 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Klebsiella phage RAN69 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
4CTFFIND4CTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 53029
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25878 / Symmetry type: POINT

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