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- EMDB-67095: Structure of the Portal and Adaptor Proteins of the Phage Phikz -

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Basic information

Entry
Database: EMDB / ID: EMD-67095
TitleStructure of the Portal and Adaptor Proteins of the Phage Phikz
Map dataPortal and adaptor of phiKZ
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ042
    • Protein or peptide: PHIKZ129
Keywordsportal / adaptor / VIRAL PROTEIN
Function / homology: / Family of unknown function (DUF7484) / PHIKZ129 / PHIKZ042
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 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_67095.png

Downloads & links

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Map

FileDownload / File: emd_67095.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPortal and adaptor of phiKZ
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 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: 0.268
Minimum - Maximum-0.8342454 - 1.3450818
Average (Standard dev.)-0.0002935558 (±0.07190473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67095_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2

Fileemd_67095_half_map_1.map
AnnotationHalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1

Fileemd_67095_half_map_2.map
AnnotationHalf 1
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: PHIKZ042
    • Protein or peptide: PHIKZ129

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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: PHIKZ042

MacromoleculeName: PHIKZ042 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 30.284676 KDa
SequenceString: MNPITKALRD ISFKIPKQIL NTVFLSSEMS GCGAAISLET RIREAVIEPR VMLDIDLVGG SKVFIPLDFP VQAEYVDPYT VVYYIPDEY TQQRPIIQCY SIHFGVLGFH TAGYAMHYNE SSMGALTRRV LDSARQLPVA QTAYINLINP HTVMVRYINI P NYSSFLAC ...String:
MNPITKALRD ISFKIPKQIL NTVFLSSEMS GCGAAISLET RIREAVIEPR VMLDIDLVGG SKVFIPLDFP VQAEYVDPYT VVYYIPDEY TQQRPIIQCY SIHFGVLGFH TAGYAMHYNE SSMGALTRRV LDSARQLPVA QTAYINLINP HTVMVRYINI P NYSSFLAC RVGNDEELNT IRPTAIPAFS KLIEYAVKSY IYNELFVSMG EAQLSGGAEL GVFRDKVYEY ADAEELYQEQ LM RWMKISR QFNDPEGKRH HIRTITAAQ

UniProtKB: PHIKZ042

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Macromolecule #2: PHIKZ129

MacromoleculeName: PHIKZ129 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 100.427438 KDa
SequenceString: MAIPGVNEGR YEPLANLQVG GQYPTPLAAT IAKLRHDPKE AGASTNNPRI VVDQHQLQKL SRETSQNIID SDSIMQVLPD LELTETVLV GSILSPKDLA EADLTFYCDQ DIFDSEIGRL LIEPVERYFK QDYKINERLD LMLRDILYHK GSSVLAVLPE N VLDAIVNG ...String:
MAIPGVNEGR YEPLANLQVG GQYPTPLAAT IAKLRHDPKE AGASTNNPRI VVDQHQLQKL SRETSQNIID SDSIMQVLPD LELTETVLV GSILSPKDLA EADLTFYCDQ DIFDSEIGRL LIEPVERYFK QDYKINERLD LMLRDILYHK GSSVLAVLPE N VLDAIVNG RREVSMESYA MVRNNLNKGR PLGILGHPTN SRISMEGHNL NNDNSNYICG DKLLSVTDNI DVLKAPHLSN RI RRKLITN KLRKYNTSLV SIATETHHFT NDQINELYQK SRGGVEYTQV ISSPKFMGRS SVGHPLILPL PSEAVIPVYV PGR PYEHVG YFLLVDLNGY PVCKEATRDF YGELQSGWQN GRSQDNSSEI LRLTRDALGI NKSNYTELEQ HQINDAYAGI IVNE LQNRL RNGMYDEELE VGLDEEIKRI MLYRSWKGKQ TQLVFIPAEM MVYVAFNYNR HGIGETQLER SKLLATMRST LLMAD VMGG MRNAVGRKRV TIHLDPDDPD PEDTVQHVQS SIMEMAHRGF PLASPDPSQA MDSLMRSGYD FKIDPGDNPG YASTAV DFD DYNTNVQAGN PELQDRLRRM HISSMGVPPE KVDPMTSPDF ATGLVQNDLV FSRRVREYQR EFCNKITKLV KIFSANS SI IRKEMVEIIS ANVGMLDTPI FKDLSVDEVI DEFIESIYVT LPAPDNTQHT RQIDALEEYS RLLDLVLSAK ITPDLFSD E MLGVSGAAEK YLAAAKSYFL RQFIAEQNIL PETKVLEELD GDDKPAFSLL DWLNNIQKTQ GSAFLEFIKG EAEIKKRLD AEYKKYRSDM DELTGGGSGG YGDFGSDMDD SSDDLGSGGN KMEAGFDTQA GYDDLSESEL TPTDEDEVDM EGLSDPAAAA EAEELEDES TESDEIG

UniProtKB: PHIKZ129

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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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 31906
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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