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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: 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: 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

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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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