9XPS | pdb_00009xps

The neck structure of the Phage Phikz


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural atlas of the intact jumbo phage phiKZ.

Xiao, H.Peng, Z.Zhou, J.Chen, Y.Peng, Y.Tang, Y.Li, T.Chen, W.Huang, S.Y.Cheng, L.Liu, H.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-71561-2
  • Primary Citation Related Structures: 
    9XPE, 9XPF, 9XPG, 9XPH, 9XPS, 9XQD, 9XQS

  • PubMed Abstract: 

    Jumbo phage phiKZ, a key model for studying phage nucleus formation and bacterial defense mechanisms, possesses a highly complex tail machine that is essential for infection. Here, we present the structural atlas of the intact jumbo phage phiKZ by cryo-EM, thereby identifying 40 constituent proteins and unveiling its modular architecture. The virion, with a length of approximately 360 nm, is comprised of an icosahedral capsid of 2520 polypeptide chains from 11 proteins, and a massive tail machine of over 900 polypeptide chains from 29 proteins. The tail features a unique, multi-layered neck and a highly elaborate baseplate. The neck is reinforced by whisker-like proteins and anchors the contractile tail, which terminates in the baseplate. The baseplate is constituted by a central hub, an inner periphery of interlocking wedge heterotrimers and hexagonal rings, and an outer periphery with a striking hexagonal star configuration. This intricate peripheral region of the baseplate serves as an extended platform for twelve peripheral fibers, which mediate host cell adsorption. Our findings provide a structural framework for understanding jumbo phage assembly and infection, thus contributing to the foundation for future functional studies and rational engineering of these phages for potential therapeutic applications.


  • Organizational Affiliation
    • Institute of Interdisciplinary Studies, Hunan Normal University, Changsha, China.

Macromolecule Content 

  • Total Structure Weight: 583.99 kDa 
  • Atom Count: 37,802 
  • Modeled Residue Count: 4,640 
  • Deposited Residue Count: 5,069 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ099
A, B
469Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD63 (Pseudomonas phage phiKZ)
Explore Q8SD63 
Go to UniProtKB:  Q8SD63
Entity Groups
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UniProt GroupQ8SD63
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ029C [auth x]695Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDD3 (Pseudomonas phage phiKZ)
Explore Q8SDD3 
Go to UniProtKB:  Q8SDD3
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UniProt GroupQ8SDD3
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ030D [auth y],
E [auth z]
293Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDD2 (Pseudomonas phage phiKZ)
Explore Q8SDD2 
Go to UniProtKB:  Q8SDD2
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UniProt GroupQ8SDD2
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ098F [auth w]542Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD64 (Pseudomonas phage phiKZ)
Explore Q8SD64 
Go to UniProtKB:  Q8SD64
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UniProt GroupQ8SD64
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ034256Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDC8 (Pseudomonas phage phiKZ)
Explore Q8SDC8 
Go to UniProtKB:  Q8SDC8
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UniProt GroupQ8SDC8
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Endolysin gp144O [auth S]260Pseudomonas phage phiKZMutation(s): 0 
EC: 4.2.2
UniProt
Find proteins for Q8SD18 (Pseudomonas phage phiKZ)
Explore Q8SD18 
Go to UniProtKB:  Q8SD18
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UniProt GroupQ8SD18
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China12034006
National Natural Science Foundation of China (NSFC)China32430020
National Natural Science Foundation of China (NSFC)China32200994

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-11
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Data collection, Database references