[English] 日本語
Yorodumi
- EMDB-62664: Cryo-EM structure of bacteriophage T1 capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62664
TitleCryo-EM structure of bacteriophage T1 capsid
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: cement protein II
    • Protein or peptide: BIG2 domain-containing protein
Keywordscapsid / phage / Viral gene product / VIRAL PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF2184 / Major capsid protein / : / Structural cement protein (E217 gp24/Pam3 gp6) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Major capsid protein / BIG2 domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen Y / 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: Viruses / Year: 2025
Title: The In Situ Structure of T-Series T1 Reveals a Conserved Lambda-Like Tail Tip.
Authors: Yuan Chen / Hao Xiao / Junquan Zhou / Zeng Peng / Yuning Peng / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of ...It is estimated that over 60% of known tailed phages are siphophages, which are characterized by a long, flexible, and non-contractile tail. Nevertheless, entire high-resolution structures of siphophages remain scarce. Using cryo-EM, we resolved the structures of T-series siphophage T1, encompassing its head, connector complex, tail tube, and tail tip, at near-atomic resolution. The density maps enabled us to build the atomic models for the majority of T1 proteins. The T1 head comprises 415 copies of the major capsid protein gp47, arranged into an icosahedron with a triangulation number of seven, decorated with 80 homologous trimers and 60 heterotrimers along the threefold and quasi-threefold axes of the icosahedron. The T1 connector complex is composed of two dodecamers (a portal and an adaptor) and two hexamers (a stopper and a tail terminator). The flexible tail tube comprises approximately 34 hexameric rings of tail tube. The extensive disulfide bond network along the successive tail rings may mediate the flexible bending. The distal tip of T1, which is cone-shaped and assembled by proteins gp33, gp34, gp36, gp37, and gp38, displays structural similarity to that of phage lambda. In conjunction with previous studies of lambda-like siphophages, our structure will facilitate further exploration of the structural and mechanistic aspects of lambda-like siphophages.
History
DepositionDec 10, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62664.png

Downloads & links

-
Map

FileDownload / File: emd_62664.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: 4.5
Minimum - Maximum-8.748673999999999 - 21.974495000000001
Average (Standard dev.)-0.0026339262 (±0.8845271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_62664_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62664_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage T1

EntireName: Escherichia phage T1 (virus)
Components
  • Complex: Escherichia phage T1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: cement protein II
    • Protein or peptide: BIG2 domain-containing protein

-
Supramolecule #1: Escherichia phage T1

SupramoleculeName: Escherichia phage T1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T1 (virus)

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 35.329426 KDa
SequenceString: MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP ...String:
MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP NITKITSGKW IDVSTMKPET AEAELTQAIE TIETITRGQH RATNILIPPS MRKVLAIRMP ETTMSYLDYF KS QNSGIEI DSIAELEDID GAGTKGVLVY EKNPMNMSIE IPEAFNMLPA QPKDLHFKVP CTSKCTGLTI YRPMTIVLIT GV

UniProtKB: Major capsid protein

-
Macromolecule #2: cement protein II

MacromoleculeName: cement protein II / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 17.022135 KDa
SequenceString:
MAQINASYQR DMAIALPGMV ADTSKYNIDG ACVVNEGDVL VGAAVQVVQA QAVDGHKLVK ALTTGTTPYG VAIRSHWQTV NAQNQMIYE DGGAINVMTS GRVWMLSKST EAPTFGSAVK LDVDGQEKSD GTIETTWTYA GGWTKYKDIQ LVEVQLHQL

UniProtKB: Uncharacterized protein

-
Macromolecule #3: BIG2 domain-containing protein

MacromoleculeName: BIG2 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 26.605688 KDa
SequenceString: MAYENLMLRP ACPGNLSDTS TYNIDGACVA QGDIEFGSAV QVVGIVDGVK VVTALSDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWALTSLDE APSLFSKLQF GSGGVVTGGS GYAGWTFAGG FVKHEDGYII EVRVKQNAFI VPPPPPPVVL V ESATITTD ...String:
MAYENLMLRP ACPGNLSDTS TYNIDGACVA QGDIEFGSAV QVVGIVDGVK VVTALSDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWALTSLDE APSLFSKLQF GSGGVVTGGS GYAGWTFAGG FVKHEDGYII EVRVKQNAFI VPPPPPPVVL V ESATITTD KESPQPNNVT IQCVANALPA NATDKTGKWS IDATNIATVN PDSGLVTPVG GEVVGDFNIT WTANDASKTT AT IAYRVEA VPTPEVDV

UniProtKB: BIG2 domain-containing protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 4.0 µm / Nominal defocus min: 2.0 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320031
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

+
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