[English] 日本語
Yorodumi
- EMDB-64745: C12 portal complex of the bacteriophage E1004 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64745
TitleC12 portal complex of the bacteriophage E1004
Map data
Sample
  • Complex: Escherichia phage
    • Protein or peptide: Portal protein
KeywordsComplex / Viral protein
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEscherichia phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsSun BN / Liu HR
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)32071209 China
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structure of drug-resistant Escherichia coli phage E1004 reveals a conserved cylindrical core among podophages.
Authors: Binning Sun / Jing Zheng / Yuan Fu / Fengyuan Tian / Hao Xiao / Su Li / Lingpeng Cheng / Ping Chen / Hongrong Liu /
Abstract: Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution ...Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution structures of near-complete cores remain scarce. Here, we present the near-atomic-resolution cryo-electron microscopy (cryo-EM) structure of the drug-resistant E. coli phage E1004, which features a T7-like core-portal-tail structure with six P22-like tailspikes. We found that the cylindrical core comprises four proteins: gp17, gp27, gp28, and gp29. Gp29 forms a tetramer, while gp28 and gp27 assemble into octamers. Notably, there are sixteen copies of gp17 in two conformations, distinct from the small core protein gp6.7 in T7. The gp17-gp27 complex reveals the mechanism for mediating the symmetry adjustment at the core-portal interface. Moreover, comparative analysis with other podophage cores highlights diversity in core protein composition and organization, particularly among the small core proteins. We propose that these variations represent evolutionary adaptations to diverse host envelopes.
History
DepositionMay 21, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64745.png

Downloads & links

-
Map

FileDownload / File: emd_64745.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.84055203 - 1.4142532
Average (Standard dev.)0.0010172278 (±0.07182403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64745_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64745_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage

EntireName: Escherichia phage (virus)
Components
  • Complex: Escherichia phage
    • Protein or peptide: Portal protein

-
Supramolecule #1: Escherichia phage

SupramoleculeName: Escherichia phage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage (virus)

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1
Details: The sequence of organism Saccharomyces cerevisiae is not available during the biocuration, replaced by A0A1S6KVI5 temporarily.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 57.330652 KDa
SequenceString: MAEREGFAAE GAKAVYDRLK NGRQPYETRA QNCAAVTIPS LFPKESDNSS TEYTTPWQAV GARCLNNLAA KLMLALFPQS PWMRLTVSE YEAKTLSQDS EAAARVDEGL AMVERVLMAY METNSFRVPL FEALKQLIVS GNCLLYIPEP EQGTYSPMRM Y RLVSYVVQ ...String:
MAEREGFAAE GAKAVYDRLK NGRQPYETRA QNCAAVTIPS LFPKESDNSS TEYTTPWQAV GARCLNNLAA KLMLALFPQS PWMRLTVSE YEAKTLSQDS EAAARVDEGL AMVERVLMAY METNSFRVPL FEALKQLIVS GNCLLYIPEP EQGTYSPMRM Y RLVSYVVQ RDAFGNILQI VTLDKVAFSA LPEDVKSQLN ADDYEPDTEL EVYTHIYRQD DEYLRYEEVE GIEVAGTEGS YP LTACPYI PVRMVRLDGE DYGRSYCEEY LGDLNSLETI TEAITKMAKV ASKVVGLVNP NGITQPRRLN KAATGEFVAG RVE DINFLQ LTKGQDFTIA KSVADAIEQR LGWAFLLNSA VQRNAERVTA EEIRYVAGEL EATLGGVYSV QSQELQLPIV RVLM NQLQS AGMIPDLPKE AVEPTVSTGL EALGRGQDLE KLTQAVNMMT GLQPLSQDPD INLPTLKLRL LNALGIDTAG LLLTQ DEKI QRMAEQSSQQ AVVQGASAAG ANMGAAVGQG AGEDMAQA

UniProtKB: Portal protein

-
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: FEI FALCON IV (4k x 4k) / Average electron dose: 32.0 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: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54423
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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