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- EMDB-60712: Structure of bacteriophage T5 tail tube -

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Basic information

Entry
Database: EMDB / ID: EMD-60712
TitleStructure of bacteriophage T5 tail tube
Map data
Sample
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Tail tube protein pb6
KeywordsComplex / VIRAL PROTEIN
Function / homologyvirus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / virus tail / viral release from host cell by cytolysis / Tail tube protein pb6
Function and homology information
Biological speciesEscherichia phage T5 (virus)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsPeng YN / 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
DepositionJul 8, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60712.png

Downloads & links

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Map

FileDownload / File: emd_60712.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å		1.3 Å/pix.
x 200 pix.
= 260. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.10531713 - 0.1571061
Average (Standard dev.)-0.0052007237 (±0.008561576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60712_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_60712_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Tail tube protein pb6

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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

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Macromolecule #1: Tail tube protein pb6

MacromoleculeName: Tail tube protein pb6 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 50.459215 KDa
SequenceString: MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT ...String:
MSLQLLRNTR IFVSTVKTGH NKTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAEW SFSTYILPYK DKNTSKQIV PDYMLWHALS SGRAINLEGT TGAHNNATNF MVNFKDNSYH ELAMLHIYIL TDKTWSYIDS CQINQAEVNV D IEDIGRVT WSGNGNQLIP LDEQPFDPDQ IGIDDETYMT IQGSYIKNKL TILKIKDMDT NKSYDIPITG GTFTINNNIT YL TPNVMSR VTIPIGSFTG AFELTGSLTA YLNDKSLGSM ELYKDLIKTL KVVNRFEIAL VLGGEYDDER PAAILVAKQA HVN IPTIET DDVLGTSVEF KAIPSDLDAG DEGYLGFSSK YTRTTINNLI VNGDGATDAV TAITVKSAGN VTTLNRSATL QMSV EVTPS SARNKEVTWA ITAGDAATIN ATGLLRADAS KTGAVTVEAT AKDGSGVKGT KVITVTAGG

UniProtKB: Tail tube protein pb6

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 39.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 40 °
Applied symmetry - Helical parameters - Axial symmetry: C3 (3 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199483
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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