[English] 日本語
Yorodumi
- EMDB-60511: Structure of the bacteriophage T5 capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60511
TitleStructure of the bacteriophage T5 capsid
Map data
Sample
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decoration protein
KeywordsComplex / VIRAL PROTEIN / STRUCTURAL PROTEIN
Function / homology
Function and homology information


viral scaffold / viral capsid, decoration / T=13 icosahedral viral capsid / evasion of host immune response / viral capsid
Similarity search - Function
: / Decoration protein pb10 N-terminal domain / Phage capsid / Phage capsid family / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Decoration protein / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPeng Y / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structures of Mature and Urea-Treated Empty Bacteriophage T5: Insights into Siphophage Infection and DNA Ejection.
Authors: Yuning Peng / Huanrong Tang / Hao Xiao / Wenyuan Chen / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, ...T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, we used cryo-electron microscopy (cryo-EM) to determine the structures of mature T5 (a laboratory-adapted, fiberless T5 mutant) and urea-treated empty T5 (lacking the tip complex) at near-atomic resolutions. Atomic models of the head, connector complex, tail tube, and tail tip were built for mature T5, and atomic models of the connector complex, comprising the portal protein pb7, adaptor protein p144, and tail terminator protein p142, were built for urea-treated empty T5. Our findings revealed that the aforementioned proteins did not undergo global conformational changes before and after DNA ejection, indicating that these structural features were conserved among most myophages and siphophages. The present study elucidates the underlying mechanisms of siphophage infection and DNA ejection.
History
DepositionJun 11, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60511.png

Downloads & links

-
Map

FileDownload / File: emd_60511.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.)
1.3 Å/pix.
x 360 pix.
= 468. Å		1.3 Å/pix.
x 360 pix.
= 468. Å		1.3 Å/pix.
x 360 pix.
= 468. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-25.438354 - 43.967742999999999
Average (Standard dev.)0.014377106 (±2.1285405)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 467.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60511_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60511_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Decoration protein

-
Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2695836 / Sci species name: Escherichia phage T5 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

-
Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 50.951684 KDa
SequenceString: MTIDINKLKE ELGLGDLAKS LEGLTAAQKA QEAERMRKEQ EEKELARMND LVSKAVGEDR KRLEEALELV KSLDEKSKKS NELFAQTVE KQQETIVGLQ DEIKSLLTAR EGRSFVGDSV AKALYGTQEN FEDEVEKLVL LSYVMEKGVF ETEHGQRHLK A VNQSSSVE ...String:
MTIDINKLKE ELGLGDLAKS LEGLTAAQKA QEAERMRKEQ EEKELARMND LVSKAVGEDR KRLEEALELV KSLDEKSKKS NELFAQTVE KQQETIVGLQ DEIKSLLTAR EGRSFVGDSV AKALYGTQEN FEDEVEKLVL LSYVMEKGVF ETEHGQRHLK A VNQSSSVE VSSESYETIF SQRIIRDLQK ELVVGALFEE LPMSSKILTM LVEPDAGKAT WVAASTYGTD TTTGEEVKGA LK EIHFSTY KLAAKSFITD ETEEDAIFSL LPLLRKRLIE AHAVSIEEAF MTGDGSGKPK GLLTLASEDS AKVVTEAKAD GSV LVTAKT ISKLRRKLGR HGLKLSKLVL IVSMDAYYDL LEDEEWQDVA QVGNDSVKLQ GQVGRIYGLP VVVSEYFPAK ANSA EFAVI VYKDNFVMPR QRAVTVERER QAGKQRDAYY VTQRVNLQRY FANGVVSGTY AAS

UniProtKB: Major capsid protein

-
Macromolecule #2: Decoration protein

MacromoleculeName: Decoration protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 17.265447 KDa
SequenceString:
MIDYSGLRTI FGEKLPESHI FFATVAAHKY VPSYAFLRRE LGLSSAHTNR KVWKKFVEAY GKAIPPAPPA PPLTLSKDLT ASMSVEEGA ALTLSVTATG GTGPYTYAWT KDGSPIPDAS GATYTKPTAA AEDAGSYKVT VTDSKQVSKD STTCAVTVNP T VPGG

UniProtKB: Decoration protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN 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: 2.2 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100841
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