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- PDB-9xpg: The structure of gp139 protein of phage phikz -

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Basic information

Entry
Database: PDB / ID: 9xpg
TitleThe structure of gp139 protein of phage phikz
ComponentsPHIKZ139
KeywordsVIRAL PROTEIN / baseplate / inner peripheral
Function / homology: / Family of unknown function (DUF7208) / PHIKZ139
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsXiao, H. / Peng, Z. / Zhou, J. / Liu, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural atlas of the intact jumbo phage phiKZ.
Authors: Hao Xiao / Zeng Peng / Junquan Zhou / Yuan Chen / Yuning Peng / Yixiong Tang / Tao Li / Wenyuan Chen / Sheng-You Huang / Lingpeng Cheng / Hongrong Liu /
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 ...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.
History
DepositionNov 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHIKZ139
B: PHIKZ139
C: PHIKZ139
D: PHIKZ139


Theoretical massNumber of molelcules
Total (without water)130,7684
Polymers130,7684
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
PHIKZ139


Mass: 32691.928 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phiKZ (virus) / References: UniProt: Q8SD23
Has protein modificationY

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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: Pseudomonas phage phiKZ / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 1200 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135070 / Symmetry type: POINT
RefinementHighest resolution: 4.14 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048431
ELECTRON MICROSCOPYf_angle_d0.68311475
ELECTRON MICROSCOPYf_dihedral_angle_d5.6041167
ELECTRON MICROSCOPYf_chiral_restr0.0481334
ELECTRON MICROSCOPYf_plane_restr0.0051502

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