[English] 日本語
Yorodumi
- PDB-23sh: The composite Cryo-EM structure of the tail region of bacteriopha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 23sh
TitleThe composite Cryo-EM structure of the tail region of bacteriophage RAN69
Components
  • adaptor gp14
  • nozzle gp13
  • portal gp19
  • tail fiber gp9
  • tail spike gp1
KeywordsVIRUS / bacteriophage / RAN69 / tail
Biological speciesKlebsiella phage RAN69 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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
Other governmentA2402025
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
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
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
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: tail spike gp1
J: tail spike gp1
O: tail spike gp1
T: nozzle gp13
r: tail fiber gp9
Y: adaptor gp14
d: adaptor gp14
i: tail fiber gp9
n: tail fiber gp9
w: portal gp19
0: portal gp19


Theoretical massNumber of molelcules
Total (without water)526,87511
Polymers526,87511
Non-polymers00
Water00
1
B: tail spike gp1
J: tail spike gp1
O: tail spike gp1
T: nozzle gp13
r: tail fiber gp9
Y: adaptor gp14
d: adaptor gp14
i: tail fiber gp9
n: tail fiber gp9
w: portal gp19
0: portal gp19
x 11


Theoretical massNumber of molelcules
Total (without water)5,795,625121
Polymers5,795,625121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation10

-
Components

#1: Protein tail spike gp1


Mass: 60926.059 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#2: Protein nozzle gp13


Mass: 86632.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#3: Protein tail fiber gp9


Mass: 32818.289 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#4: Protein adaptor gp14


Mass: 21286.904 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
#5: Protein portal gp19


Mass: 58217.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Klebsiella phage RAN69 (virus)
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

EM software
IDNameVersionCategory
1RELION4particle selection
2PHENIX1.19.2_4158model refinement
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 53029
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53029 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237217
ELECTRON MICROSCOPYf_angle_d0.44150633
ELECTRON MICROSCOPYf_dihedral_angle_d3.9395235
ELECTRON MICROSCOPYf_chiral_restr0.0435749
ELECTRON MICROSCOPYf_plane_restr0.0046623

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more