[English] 日本語
Yorodumi
- EMDB-67098: The structure of baseplate central region of phage phikz -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67098
TitleThe structure of baseplate central region of phage phikz
Map data
Sample
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ101
    • Protein or peptide: PHIKZ174
    • Protein or peptide: PHIKZ164
    • Protein or peptide: PHIKZ163.1
Keywordsspike / VIRAL PROTEIN
Function / homologymetal ion binding / PHIKZ163.1 / PHIKZ174 / PHIKZ164 / PHIKZ101
Function and homology information
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 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

-
Structure visualization

Supplemental images

emd_67098.png

Downloads & links

-
Map

FileDownload / File: emd_67098.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. Å		1.36 Å/pix.
x 300 pix.
= 408. 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: 0.2
Minimum - Maximum-0.42429847 - 0.8199702
Average (Standard dev.)0.006142746 (±0.0716721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_67098_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_67098_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_67098_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pseudomonas phage phiKZ

EntireName: Pseudomonas phage phiKZ (virus)
Components
  • Complex: Pseudomonas phage phiKZ
    • Protein or peptide: PHIKZ101
    • Protein or peptide: PHIKZ174
    • Protein or peptide: PHIKZ164
    • Protein or peptide: PHIKZ163.1

-
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)

-
Macromolecule #1: PHIKZ101

MacromoleculeName: PHIKZ101 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 52.013387 KDa
SequenceString: MAVDASSLMR EVDTIINSAN NYSAYKIEAK ILVGDFDWVV PLRVDYFDTF RNYADGSYGD LILTELLIGT GDFQFDILPR RDELRCDVK FIPLLPNSSL LDTSRKASVK RYRCFVVLSP EDDITLTNKQ SQLTSKEAMN QISYKPYRFQ LVEESVYQSL M ITIGKNFT ...String:
MAVDASSLMR EVDTIINSAN NYSAYKIEAK ILVGDFDWVV PLRVDYFDTF RNYADGSYGD LILTELLIGT GDFQFDILPR RDELRCDVK FIPLLPNSSL LDTSRKASVK RYRCFVVLSP EDDITLTNKQ SQLTSKEAMN QISYKPYRFQ LVEESVYQSL M ITIGKNFT NVTTADVLRA FLKQSISQLT EADDNRVIDI NMEPGWNTEV RPVIPIPDGT PLKDLPNILQ NKEGGVYATG LG RYIQGSY LYVYSLYDTK KYQKGAKTLN IINVPNDRLY GVEKTYVNGD TYTTILATGD ASSLDKALYE MVDNGSGYRF ADA NKLLDD FTISKDNKML VDAASNLYEV RGDGLKTGFQ NIQWTKQRST SNPFKHYTEL AKRQGQFLKI QWNHGDADIL TPGM PVKFQ TVDNNVVKTY YGVLLGVDEQ FAAGDNNPNP HRYVCVVTLA IFLNRSDQNE IEPST

UniProtKB: PHIKZ101

-
Macromolecule #2: PHIKZ174

MacromoleculeName: PHIKZ174 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 39.125891 KDa
SequenceString: MVDFALPSFI GTGKDEVAKI DAYTEVSSDV RNSLVSGISN FEQGFSGILN RTLKAVRGIG DLIPSDGINL ADASRRIQGA LKGSRSDLQ NIAQSLENII FGELTGSNGG PGYVQQATRM ANEVKMIING VDVYKQNSNY QNMSSILSFL EDMSGSNAII K FFDLGAEA ...String:
MVDFALPSFI GTGKDEVAKI DAYTEVSSDV RNSLVSGISN FEQGFSGILN RTLKAVRGIG DLIPSDGINL ADASRRIQGA LKGSRSDLQ NIAQSLENII FGELTGSNGG PGYVQQATRM ANEVKMIING VDVYKQNSNY QNMSSILSFL EDMSGSNAII K FFDLGAEA AVLRGVLQEV AQWGIPDLID DTFGATKRYD GSGNWVGYDY KYNDDFRFTL TKRTADSLGN NIDLDVIDRI IT HSGAEAL TADVPDYPNR IIANYVFPEG TKPEDYPTIL SKLVSIMDKL KPDWFWTLRN TQKVFNFGVL QTASDDATTL FLS NDTYRT PMLVAPFYKP AQALELFRDM YPMIAIPT

UniProtKB: PHIKZ174

-
Macromolecule #3: PHIKZ164

MacromoleculeName: PHIKZ164 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 32.434172 KDa
SequenceString: MDEAVSLLSN MQDSEIQTSE FRLWSIGRAT ENKPRNSFTL MVLPIESATA TDGETTFNPV EEVVDGVDAD GRAYTTKVSV SRDIPCIWL PNEDNRATPP DVMRGEKIAI YRLGDTSQFY WRSMGLSNDL RTLESVVYTF NASLSPGGAG KNFDTCYFMQ F SAHDKHVT ...String:
MDEAVSLLSN MQDSEIQTSE FRLWSIGRAT ENKPRNSFTL MVLPIESATA TDGETTFNPV EEVVDGVDAD GRAYTTKVSV SRDIPCIWL PNEDNRATPP DVMRGEKIAI YRLGDTSQFY WRSMGLSNDL RTLESVVYTF NASLSPGGAG KNFDTCYFMQ F SAHDKHVT IGTSKANGEP YRYSVQINTG TGAVYILDDI GNRFELVSKD KRLMLMNADN SFVKVEKKAI DLNADQYIKL TS GGSTLEL NPTEFKVNTT NTTIKSSGTH IQEAGGTMTH KAGGNMLFTA PRYDFT

UniProtKB: PHIKZ164

-
Macromolecule #4: PHIKZ163.1

MacromoleculeName: PHIKZ163.1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 8.809327 KDa
SequenceString:
MPGIAVCNMD SAGGVILPGP NVKCFYKGQP FAVIGCAVAG HGRTPHDSAR MIQGSVKMAI AGIPVCLQGS MASCGHTATG RPNLTCGS

UniProtKB: PHIKZ163.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27796
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more