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- EMDB-67111: The structure of outer peripheral region in the phage phiKZ basep... -

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Basic information

Entry
Database: EMDB / ID: EMD-67111
TitleThe structure of outer peripheral region in the phage phiKZ baseplate complex
Map data
Sample
  • Virus: Pseudomonas phage phiKZ (virus)
    • Protein or peptide: PHIKZ026
    • Protein or peptide: PHIKZ027
    • Protein or peptide: PHIKZ127
    • Protein or peptide: PHIKZ130
    • Protein or peptide: PHIKZ139
    • Protein or peptide: PHIKZ157
Keywordsbaseplate / outer peripheral / VIRAL PROTEIN
Function / homology
Function and homology information


: / : / Family of unknown function (DUF7193) / Family of unknown function (DUF7941) / : / Family of unknown function (DUF7208)
Similarity search - Domain/homology
PHIKZ157 / PHIKZ139 / PHIKZ130 / PHIKZ127 / PHIKZ027 / PHIKZ026
Similarity search - Component
Biological speciesPseudomonas phage phiKZ (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.53 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 18, 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_67111.png

Downloads & links

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Map

FileDownload / File: emd_67111.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 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-0.40225008 - 0.8538703
Average (Standard dev.)-0.00009199765 (±0.036300912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67111_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_67111_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
  • Virus: Pseudomonas phage phiKZ (virus)
    • Protein or peptide: PHIKZ026
    • Protein or peptide: PHIKZ027
    • Protein or peptide: PHIKZ127
    • Protein or peptide: PHIKZ130
    • Protein or peptide: PHIKZ139
    • Protein or peptide: PHIKZ157

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Supramolecule #1: Pseudomonas phage phiKZ

SupramoleculeName: Pseudomonas phage phiKZ / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2905945 / Sci species name: Pseudomonas phage phiKZ / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: PHIKZ026

MacromoleculeName: PHIKZ026 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 62.04757 KDa
SequenceString: MTTSYESSQY QPPQHKNHFW FRGDIVSYAG ETGKAIPAKG DLVFDAAQGW FIVREVDETT GVSILDPWYM PQKPGNENEQ NLLVAVGPG YSSESYRLFL DQSVTPFNIC PDRRLHFYGS MVHGYKVFLG SDISEIHGKV ISLFYDNAGN YLGPTIPVES V PDPLTQQN ...String:
MTTSYESSQY QPPQHKNHFW FRGDIVSYAG ETGKAIPAKG DLVFDAAQGW FIVREVDETT GVSILDPWYM PQKPGNENEQ NLLVAVGPG YSSESYRLFL DQSVTPFNIC PDRRLHFYGS MVHGYKVFLG SDISEIHGKV ISLFYDNAGN YLGPTIPVES V PDPLTQQN VVKALMNGRT AEKMQNGERV TLVAYDDVGG PVSIAQLVVM NTEVIAQEDT SKKYVGGITI ESPFISPADP KV IEFPLNV PVESLPMMGA VHYRDGKKHV MNIDGTAMAI YGLRNYIATE EGQEFKLTLS YQLAQDELSY LSTPSANRRI QET YTARTT PVQGAYSCRM FVYPAWVNEA VGYRLEFWLA NIDRQQIWNI TPYVELGANS APFNPRGYGT IQTLTYAVNL NQVD GRFLP VRFASTFQVA LLSAGNNRNA NWEIYSRPDQ GEAYGRDLKA DIEFINGNLW DLRLANGAQS QAAWLKKMYF AAEPL TGPM EATPPTPTHF RVRTVHNEYE YTVSQWNTAL RINAQDMADG ALLQITWIRR EYDTDLQLAI TALPCLQR

UniProtKB: PHIKZ026

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Macromolecule #2: PHIKZ027

MacromoleculeName: PHIKZ027 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 105.36418 KDa
SequenceString: MNAYLLRHAI DNVWCNPAQD RQFVYELKQL TPRYGVRVNW VVDYTRYKLP VQSTRDYWHL YQIGKMIPKH LGLPKVYNKW MSLNELAQN HLNLADVYVN SGINYSRNDT YVLITSSQNL LIAVKIDPLF PDLDENQPYL HVYNNAYFQS NRSDVAGHRW L VSESYRVK ...String:
MNAYLLRHAI DNVWCNPAQD RQFVYELKQL TPRYGVRVNW VVDYTRYKLP VQSTRDYWHL YQIGKMIPKH LGLPKVYNKW MSLNELAQN HLNLADVYVN SGINYSRNDT YVLITSSQNL LIAVKIDPLF PDLDENQPYL HVYNNAYFQS NRSDVAGHRW L VSESYRVK TISELTQFQI KIMDTIASKG GVPKYFVNGR YVNEISPVTA TVGDVCDFIL DPSIKRMVDF DLRTLPVFMS EI DSERKYI LHYTDKTVQT IEFFDDVEAY IYQPLGNNRY TGVNYHHNES RWMRMLTHKD YSIPTARIDQ FKALHPEDPR RGA DPTRWP SQNWKALDNL VFRIYIHHSG YDRPLVADSH RIQILYRLKS EDIIRAMTGA DSGNPLWRAE NLEQSPYCWF MSAP SSFVY PLTFNLPEET SPSKVEAQNM AGDVFGYYEA ANIQGYNPAW VYNDAGLKTA DLRYNYWLDA TVFEYDEKGI LLGYN YHTA GRKYFPKDSR CAYVECINGK GSVDLHEAYG NDPVPLRDGD NWRVYVSPVW AGVPTGEWQD ITDHPDRNNW GFYDDT TDD KRWVWIAKSN EWYGLVRTDE YFYLKELKFN KTDGIIKWSI RNTETHNGVK VDKLMEIPFG QYDVFVNGRP IIEGLDY TR EWPQTVLCNL EYLNADPNAV NTILLRGTGF PTPDLKPYEP GEIGFIEYGV LSNDGIYKVH SNKQSRIIID GHYRDPAD L EFQEDQGTTV ITDERNGAPF QIQTPQARFR DVYNDDYQAR IKDDARDKQV TDFMTEYFPM KPQPNPDKID YRYQVLSAF SCKIIHDIVK EYIKPPYQNG RYSDDDIVKQ LKDYEWLAAY DIINKGYNKN KVVVYPHWYT EPVELDIFQW EYLNRILSIY LREVPPLSL FVKIKRNQP

UniProtKB: PHIKZ027

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Macromolecule #3: PHIKZ127

MacromoleculeName: PHIKZ127 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 33.643703 KDa
SequenceString: MFITRDYCKV DPWTAIVEMI NNNYMYQLTP GTCKLLEFEA IDHKRTRIKI DPCRDNKPGE LLPVVERTEF FYQRLDFNEF FKVPQVVEV KDVYLPFTTL DLAKLICEKN DIKFDLDDFY HQEINSYNQD VTITCNPDSL RFVGEFKIKL INTVRQDISL L TKVNSFPT ...String:
MFITRDYCKV DPWTAIVEMI NNNYMYQLTP GTCKLLEFEA IDHKRTRIKI DPCRDNKPGE LLPVVERTEF FYQRLDFNEF FKVPQVVEV KDVYLPFTTL DLAKLICEKN DIKFDLDDFY HQEINSYNQD VTITCNPDSL RFVGEFKIKL INTVRQDISL L TKVNSFPT IVKWPAGNGN KPTAEFITMS LDFTDYRSFL LPIKAFKENP YSLEMAAILK KVTGLDFVAK SNATDYNITN IV RNGVNNF IVDYNGPVVP AYSLRNDITN VMVLRLSKTM CPNINGRLLI HYN

UniProtKB: PHIKZ127

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Macromolecule #4: PHIKZ130

MacromoleculeName: PHIKZ130 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 48.65134 KDa
SequenceString: MYTLVRSRHR IDRKSGRWTD VDLANEKIST LSVKFGDIYL YIEYPGPTAP ILNALHWVNV TNEISSANPD LTVQEWLTSL GDKSLPFDD ELPNEKVRLV KYAQAWHAGY IAQPVARNGH VTDGGSKFKK EDILLTHPKH KPEDVCRKCL ITVNTMFHLA D YTSAGVRI ...String:
MYTLVRSRHR IDRKSGRWTD VDLANEKIST LSVKFGDIYL YIEYPGPTAP ILNALHWVNV TNEISSANPD LTVQEWLTSL GDKSLPFDD ELPNEKVRLV KYAQAWHAGY IAQPVARNGH VTDGGSKFKK EDILLTHPKH KPEDVCRKCL ITVNTMFHLA D YTSAGVRI IDGNKTVRTA NDNQIGLYSF ETIGDIKYVP IKTDMIYPQQ VGAPLFDATY IDMPEDIDLT NKTILLSLGG YL CVLGKGF NRVGVRTWRV DFGSLSMFDR YMQSRELIDL SSLGLEIDDK NKTLLSVEQI KKDSVIKAYM TLSQTFFIVL DSP SLFQEF VPLEPLKLPG RYQATNTRTE VYPKYTKPDQ LPVVGAHGKM LDYHFIHEDK HSVYCCTLNI RNNFDAHTHD WKTE KVVDG GRYPAWPFVH DTAYLRILGV DG

UniProtKB: PHIKZ130

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Macromolecule #5: PHIKZ139

MacromoleculeName: PHIKZ139 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / 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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Macromolecule #6: PHIKZ157

MacromoleculeName: PHIKZ157 / type: protein_or_peptide / ID: 6 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage phiKZ (virus)
Molecular weightTheoretical: 51.155703 KDa
SequenceString: MYNLKGFYEY PSLIDNATDK VAKFGEISDN SATYAKDKKI LTSESTPSTA FIAFHSVRDE IPVDITAEYQ LQVLKIGEFL LKQGNSGTI GKNTTPTQVN QMLMTEFNGK LSTVRSGPIG NMNTRLYLPE YIEFSLIVTG NEPNLIRVWL ADDAFAGQYD E FKIEVVHP ...String:
MYNLKGFYEY PSLIDNATDK VAKFGEISDN SATYAKDKKI LTSESTPSTA FIAFHSVRDE IPVDITAEYQ LQVLKIGEFL LKQGNSGTI GKNTTPTQVN QMLMTEFNGK LSTVRSGPIG NMNTRLYLPE YIEFSLIVTG NEPNLIRVWL ADDAFAGQYD E FKIEVVHP IGKNAQGNYD DWFKDPLEVK KLLDKFDLPT KLEEVQAKRA QYPYTYQNAY RFDYHNPRDD TMQFPAYWIV II YGVAGNN LDIIKDAICD ELLDGSAHTR EEWEKILPEL FRTTEFIICP FWNQLALENS DFRGGIYSPI IDPRKRIALM RRT ARGSGY TTTYFDSHYE LSCNIYRSVG FSVIGNAKNR NNLTQFSQVF PDYIIATNTS EDINRISVET REFLLVFADL LKAA EDMDR YTTVPMGMSR MIRDDVIYAA KVYKNINYMV VTRKSVEQFG

UniProtKB: PHIKZ157

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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: 4.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131125
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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