[English] 日本語
Yorodumi
- EMDB-67096: The structure of sheath and tube proteins of phage Phikz -

+
Open data


ID or keywords:

Loading...

-
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: 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

-
Structure visualization

Supplemental images

emd_67096.png

Downloads & links

-
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

Size
Brightness
Contrast
Others
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

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: 0.46
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 °

-
Supplemental data

-
Mask #1

Fileemd_67096_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_67096_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_67096_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: PHIKZ029
    • Protein or peptide: PHIKZ030

-
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: 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

-
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

-
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: 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)

+
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