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- EMDB-67097: The structure of gp139 protein of phage phikz -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-67097
TitleThe structure of gp139 protein of phage phikz
Map data
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ139
Keywordsbaseplate / inner peripheral / VIRAL PROTEIN
Function / homology: / Family of unknown function (DUF7208) / PHIKZ139
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 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: To Be Published
Title: Structural atlas of the intact jumbo phage phiKZ
Authors: Xiao H / Peng Z / Zhou J / Liu H
History
DepositionNov 16, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67097.png

Downloads & links

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Map

FileDownload / File: emd_67097.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.4420112 - 0.84090865
Average (Standard dev.)0.0044271154 (±0.052845083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67097_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67097_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: PHIKZ139

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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: PHIKZ139

MacromoleculeName: PHIKZ139 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 32.691928 KDa
SequenceString: MSAIDQQYIN VTRTAYGSYL QTCKYLGIPF KLIPNTTLNE KFSIQQNVAP SAGQIPNVQY MVIGNRGHYF VKGPDGSDEV ENNIHRAND AALYNHIPFV LREVADDLPA QRRNMYRLRR LEEHNGKQYF AYYARKIDVT GVVPKLLKIT IVDGEPVVTP Y VPNRDDLN ...String:
MSAIDQQYIN VTRTAYGSYL QTCKYLGIPF KLIPNTTLNE KFSIQQNVAP SAGQIPNVQY MVIGNRGHYF VKGPDGSDEV ENNIHRAND AALYNHIPFV LREVADDLPA QRRNMYRLRR LEEHNGKQYF AYYARKIDVT GVVPKLLKIT IVDGEPVVTP Y VPNRDDLN PTPPTISNQG TVVGSNESIS ASAIVTVNLT AEEILEITTA HRIRTGSVRS PIISEIGLCS GVDKDVQGQS GA SGNFIYT EVIACQINVF IATNHAVGYN SDGLKLTFDI GGVEPMLGSK AINVAKFVPK D

UniProtKB: PHIKZ139

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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: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 135070
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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