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- PDB-23sf: Cryo-EM structure of icosahedrally averaged bacteriophage RAN69 capsid -

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Basic information

Entry
Database: PDB / ID: 23sf
TitleCryo-EM structure of icosahedrally averaged bacteriophage RAN69 capsid
Components
  • decoration protein gp5
  • decoration protein gp6
  • major capsid protein gp17
KeywordsVIRUS / bacteriophage / RAN69 / capsid
Biological speciesKlebsiella phage RAN69 (virus)
MethodELECTRON MICROSCOPY / single 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, 3items
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, 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / 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: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: decoration protein gp6
C: decoration protein gp6
I: major capsid protein gp17
B: major capsid protein gp17
K: major capsid protein gp17
D: major capsid protein gp17
E: major capsid protein gp17
F: major capsid protein gp17
G: decoration protein gp5
H: major capsid protein gp17
J: decoration protein gp5
L: decoration protein gp5


Theoretical massNumber of molelcules
Total (without water)308,34812
Polymers308,34812
Non-polymers00
Water00
1
A: decoration protein gp6
C: decoration protein gp6
I: major capsid protein gp17
B: major capsid protein gp17
K: major capsid protein gp17
D: major capsid protein gp17
E: major capsid protein gp17
F: major capsid protein gp17
G: decoration protein gp5
H: major capsid protein gp17
J: decoration protein gp5
L: decoration protein gp5
x 60


Theoretical massNumber of molelcules
Total (without water)18,500,885720
Polymers18,500,885720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein decoration protein gp6


Mass: 12978.493 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#2: Protein
major capsid protein gp17


Mass: 37696.387 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#3: Protein decoration protein gp5


Mass: 6172.131 Da / Num. of mol.: 3 / 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
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 75628
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7563 / Symmetry type: POINT

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