9XQD | pdb_00009xqd

The structure of outer peripheral region in the phage phiKZ baseplate complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.53 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: 1,217.05 kDa 
  • Atom Count: 71,157 
  • Modeled Residue Count: 8,852 
  • Deposited Residue Count: 10,710 
  • Unique protein chains: 6

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ026552Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDD6 (Pseudomonas phage phiKZ)
Explore Q8SDD6 
Go to UniProtKB:  Q8SDD6
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UniProt GroupQ8SDD6
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ027G,
H [auth K]
898Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SDD5 (Pseudomonas phage phiKZ)
Explore Q8SDD5 
Go to UniProtKB:  Q8SDD5
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UniProt GroupQ8SDD5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ127I [auth 0]290Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD35 (Pseudomonas phage phiKZ)
Explore Q8SD35 
Go to UniProtKB:  Q8SD35
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UniProt GroupQ8SD35
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ130J [auth L],
K [auth H]
427Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD32 (Pseudomonas phage phiKZ)
Explore Q8SD32 
Go to UniProtKB:  Q8SD32
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UniProt GroupQ8SD32
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ139298Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD23 (Pseudomonas phage phiKZ)
Explore Q8SD23 
Go to UniProtKB:  Q8SD23
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PHIKZ157445Pseudomonas phage phiKZMutation(s): 0 
UniProt
Find proteins for Q8SD05 (Pseudomonas phage phiKZ)
Explore Q8SD05 
Go to UniProtKB:  Q8SD05
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UniProt GroupQ8SD05
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.53 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