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- EMDB-67096: The structure of sheath and tube proteins of phage Phikz -

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Basic information

Entry
Database: EMDB / ID: EMD-67096
TitleThe structure of sheath and tube proteins of phage Phikz
Map data
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ030
Keywordssheath / tube / VIRAL PROTEIN
Function / homology: / Phage tail tube protein / : / Bacteriophage phiKZ, gp29PR / PHIKZ030 / PHIKZ029
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsXiao H / Peng Z / Zhou J / Liu H
Funding support China, 3 items
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, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67096.png

Downloads & links

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Map

FileDownload / File: emd_67096.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-1.0531534 - 1.8301661
Average (Standard dev.)0.002413197 (±0.10102161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67096_msk_1.map
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Half map: #2

Fileemd_67096_half_map_1.map
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Half map: #1

Fileemd_67096_half_map_2.map
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Sample components

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Entire : Pseudomonas phage phiKZ

EntireName: Pseudomonas phage phiKZ (virus)
Components
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ029
    • Protein or peptide: PHIKZ030

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas phage phiKZ (virus)

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Macromolecule #1: PHIKZ029

MacromoleculeName: PHIKZ029 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 77.712344 KDa
SequenceString: MAYYNAVPRV VFNGIRDRSR RPLIRPDITF AQHCPLLRLF TETGPTETTY VGDSDDGFAS IYGQASLDPR SKFFNTQSLL ALNLLGRGN GFYVKRLRPE DAANPSRLIV AIEIVEDEIP LTIRRLSGFN YPNSVRDIGN APVPTTDKVD GLKARIILIE D NTSEVGTQ ...String:
MAYYNAVPRV VFNGIRDRSR RPLIRPDITF AQHCPLLRLF TETGPTETTY VGDSDDGFAS IYGQASLDPR SKFFNTQSLL ALNLLGRGN GFYVKRLRPE DAANPSRLIV AIEIVEDEIP LTIRRLSGFN YPNSVRDIGN APVPTTDKVD GLKARIILIE D NTSEVGTQ RVLPGTLVSD KDGSQSLVYP LFEAPVSFFG KLGDSNGMRV WSTTTADIEE FDEAAMAKFK TRQFRIQLIE KP EVGTSPV IVKTADQQDY LNITFDKGVY SDMYNADLYV GDVLVDSYSD DGVVSGLSPL YSPFSQFYVY HENIDLVRQM IYD TEMRVN PAAAAHTTAP GEIDFLTFLA VDGDPYQGIQ VLGPLDGGIT LGKDGNIYAS GGTDGTTDLE EYAKLVDIEN INFG KLNDR YNNIAEYQFG VLYDTGLPME SKYRAMRVLS ARRDLQYFFT TFVETDSRLP DEATELSRVQ QIITRLKAFP ESTLY GTGV CRAMIVMQSG KLMDGTYRKY VPQLLDVAMS WARYAGAGTG NLVPGMEMDV SPNNRVTFVK DLNVKFFDDR VRAQAW ANG ATWSQSYDHR SSYYPCLRSV MLDDTSVLLS PITVNICCVL IRLIHKVHAQ FSGNATLTPE QLVERCDEYI LDLVRDM FG TRVNIIPRTE ITPIDANNGT SWTCNVTVEA NNPRTTLNFN LETVRIETPP AQQ

UniProtKB: PHIKZ029

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Macromolecule #2: PHIKZ030

MacromoleculeName: PHIKZ030 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 32.686555 KDa
SequenceString: MARYNDPMAP ETGYGAGGAR NTVNLAQAGT NVFRPDLANL ATNTPYVARN LVPFLLDAPR FFKYASNTNW LVACLKAFVE THTRTIDGL QRTLTVDNAE APWGGSGEVI QTATNVTRAR SNPNFGCWEL QNRAIQRFLQ WWINYGIADE NTKVPRIVSD G IVPVEKYD ...String:
MARYNDPMAP ETGYGAGGAR NTVNLAQAGT NVFRPDLANL ATNTPYVARN LVPFLLDAPR FFKYASNTNW LVACLKAFVE THTRTIDGL QRTLTVDNAE APWGGSGEVI QTATNVTRAR SNPNFGCWEL QNRAIQRFLQ WWINYGIADE NTKVPRIVSD G IVPVEKYD ATFYGMTVLF VEPDPTFQDC VNAYLCTNMF PLTTGPWENR KDASQIGQNL DLNVEFSALT DVSEGVQEYA RQ MFRKLNI RGMNPNNQKL DWGGLSADVL RARNGIQDQI ERAVGNRVTY DGVGLS

UniProtKB: PHIKZ030

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 26028
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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