[English] 日本語
Yorodumi
- EMDB-65451: Cyanopodophage Pan3 portal complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65451
TitleCyanopodophage Pan3 portal complex
Map data
Sample
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Portal protein
KeywordsCyanophage / Virus / Portal / VIRAL PROTEIN
Function / homology:
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHou P / Zhou CZ / Jiang YL
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
National Natural Science Foundation of China (NSFC)92451302 China
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structure of cyanopodophage Pan3 reveals a modular tail architecture for host recognition.
Authors: Pu Hou / Jie Zhu / Rong-Cheng Yu / Feng Yang / Kang Du / Jing Li / Wen-Wen Kong / Jie Wang / Yuxing Chen / Cong-Zhao Zhou / Yong-Liang Jiang /
Abstract: Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on ...Cyanophages, which are bacteriophages that specifically infect host cyanobacteria, also utilize the tail to initiate host recognition and adsorption. Owing to the limited structural information on cyanophages, our understanding of the mechanism by which cyanophages specifically recognize their hosts remains largely unknown. Here, we determined the intact cryoelectron microscopy structure of a freshwater cyanopodophage Pan3, which consists of an icosahedral shell and a short tail comprising four modular components: the dodecameric adaptor, hexameric nozzle, trimeric needle, and six heterohexameric tailspikes. Notably, each tailspike features an SGNH esterase domain fused to a lectin domain, forming a continuous groove complementary to the host lipopolysaccharide. These findings provide insights into the receptor engagement in Podoviridae, and establish a structural framework for cyanophage and host interactions that may guide future antibacterial interventions against harmful blooms.
History
DepositionJul 21, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65451.png

Downloads & links

-
Map

FileDownload / File: emd_65451.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.032668024 - 0.06292418
Average (Standard dev.)0.00004548507 (±0.0035754999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 445.12003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_65451_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65451_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pseudanabaena phage Pan3

EntireName: Pseudanabaena phage Pan3 (virus)
Components
  • Virus: Pseudanabaena phage Pan3 (virus)
    • Protein or peptide: Portal protein

-
Supramolecule #1: Pseudanabaena phage Pan3

SupramoleculeName: Pseudanabaena phage Pan3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2981586 / Sci species name: Pseudanabaena phage Pan3 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudanabaena phage Pan3 (virus)
Molecular weightTheoretical: 69.321203 KDa
SequenceString: MTSQEDYTLE ALTAAVRRFE ESEDATTEAR AAAERDRDYY DEKQWTAAEK AALERRGQPA ITFNRIKRKV NALTGIEKQT RKDPRAFPR NPDDEESAQA ATDAIRYVCE DSRWDDKRSE AAKELAIEGT CAIMVGVKQA KGGIDPDIRR IAWDRFYYDP H ATAFDFED ...String:
MTSQEDYTLE ALTAAVRRFE ESEDATTEAR AAAERDRDYY DEKQWTAAEK AALERRGQPA ITFNRIKRKV NALTGIEKQT RKDPRAFPR NPDDEESAQA ATDAIRYVCE DSRWDDKRSE AAKELAIEGT CAIMVGVKQA KGGIDPDIRR IAWDRFYYDP H ATAFDFED ACYMGVVVWM DLDKAKAKYP QAEDVLIETW RQAQQSETYD DKPKHRLWAD YRRRRVRICE EYYLDGEGWK FC MFTKAGF IVPPMPSPYI GEDGEPECPI KAVSLYIDRD NNRYGEVRTM IGPQDEINKR RSKALHLINS RQVRVSPNVQ MDA QSVRKE LSKPDGVFVG DSGEVEILPT QDMASANLAM LQEAKNEIDL LGPNAALGGK AEGQMSGRAI LAQQQGGMTE AATY LDRIR ALSIAVYRSV WARIRQVWTG ERWVRVTDNE RNLRFVGLNQ PVTMLQAMAK EMGITKDALP QLEQAAQAGD PQAMQ AMQQ LHALANDPRA NMVVGVENAV AELDVDILVD EGLDAPTIAA EEFEQLMKLA STGIVPIPPD VLIEASSLRN KPKLLE MLK QGPSQEQMMA QQIALAGEQA KVAETESKTG LNVAKTQETL ASIQTNALQA GVQAGMA

UniProtKB: UNIPROTKB: A0AA49HFY0

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 120202
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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