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- EMDB-61907: asymmetric recosntructon of DNA-ejected T7 -

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Basic information

Entry
Database: EMDB / ID: EMD-61907
Titleasymmetric recosntructon of DNA-ejected T7
Map datamismatch reconstruction
Sample
  • Virus: Escherichia phage T7 (virus)
KeywordsComplex / VIRUS
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsLiu HR / Chen WY
Funding support China, 6 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
National Natural Science Foundation of China (NSFC)32371263 China
National Natural Science Foundation of China (NSFC)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
CitationJournal: J Virol / Year: 2025
Title: Conformational changes in and translocation of small proteins: insights into the ejection mechanism of podophages.
Authors: Jing Zheng / Hao Xiao / Hao Pang / Li Wang / Jingdong Song / Wenyuan Chen / Lingpeng Cheng / Hongrong Liu /
Abstract: Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope ...Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope channel for DNA ejection. Although the core proteins of bacteriophage T7 have been resolved at near-atomic resolution, the mechanisms of core proteins and DNA ejection remain to be fully elucidated. In this study, we provided improved structures of core proteins in mature T7 and the portal-tail complex in lipopolysaccharide-induced DNA-ejected T7 to resolutions of approximately 3 Å. Using these structures, we identified three small proteins, namely gp14, gp6.7, and gp7.3, and illustrated the conformational changes in and translocation of these proteins from the mature to DNA-ejected states. Our structures indicate that gp6.7, which participates in the assembly of the core and trans-envelope channel, is a core protein, and that gp7.3 serves as a structural scaffold to assist the assembly of the nozzle into the adaptor.
IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in ...IMPORTANCE: Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in the periplasmic tunnel form in the DNA-ejected T7 have been resolved previously. Here, we resolved the structures of two new structural proteins (gp6.7 and gp7.3) within mature T7 and receptor-induced DNA-ejected T7. The gp6.7 protein participates in the assembly of the core complex within mature T7 and the trans-envelope channel during T7 infection; therefore, gp6.7 is a core protein. Before T7 infection, gp7.3 plays a role in promoting the assembly of the nozzle into the adaptor.
History
DepositionOct 13, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61907.png

Downloads & links

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Map

FileDownload / File: emd_61907.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmismatch reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.12 Å/pix.
x 640 pix.
= 1356.8 Å		2.12 Å/pix.
x 640 pix.
= 1356.8 Å		2.12 Å/pix.
x 640 pix.
= 1356.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-21.517752000000002 - 36.67756
Average (Standard dev.)-0.23921843 (±2.7540379)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1356.7999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_61907_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_61907_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage T7

EntireName: Escherichia phage T7 (virus)
Components
  • Virus: Escherichia phage T7 (virus)

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Supramolecule #1: Escherichia phage T7

SupramoleculeName: Escherichia phage T7 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10760 / Sci species name: Escherichia phage T7 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23461
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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