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- EMDB-63001: The capsid of mature phage N4 -

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Basic information

Entry
Database: EMDB / ID: EMD-63001
TitleThe capsid of mature phage N4
Map datacapsid of mature phage N4
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein
KeywordsComplex / VIRUS
Function / homologyPhage capsid protein / viral capsid / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 32 kDa protein / Major capsid protein
Function and homology information
Biological speciesEnterobacteria phage N4 (virus) / Escherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu H / Chen W
Funding support China, 7 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)32200994 China
National Natural Science Foundation of China (NSFC)32401014 China
National Natural Science Foundation of China (NSFC)32271329 China
National Natural Science Foundation of China (NSFC)32071262 China
CitationJournal: Structure / Year: 2025
Title: Asymmetric structure of podophage N4 from the Schitoviridae family reveals a type of tube-sheath short-tail architecture.
Authors: Jing Zheng / Hao Pang / Hao Xiao / Junquan Zhou / Zhonghua Liu / Wenyuan Chen / Hongrong Liu /
Abstract: The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented ...The tails of the majority of reported podophages are typically composed of an adaptor, a nozzle, and a needle, and flanked by six or twelve fibers. However, the Schitoviridae family, as represented by podophage N4, exhibits a different tail architecture that remains poorly understood. In this study, we employed cryoelectron microscopy (cryo-EM) to determine the atomic structures of mature and empty podophage N4 particles. The N4 tail, which is connected to the head by a portal and flanked by 12 fibers, comprises an adaptor, a 12-fold extended tail tube encircled by a 6-fold tail sheath, and a plug. The extended tail sheath is composed of two proteins, gp65 and gp64. Furthermore, we identified two distinct tail conformations in the mature podophage N4. Our structures provide insights into the mechanisms of ejection and early transcription of podophage N4, as well as for N4-like phages and CrAssphages.
History
DepositionJan 5, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63001.png

Downloads & links

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Map

FileDownload / File: emd_63001.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcapsid of mature phage N4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 736 pix.
= 780.16 Å		1.06 Å/pix.
x 736 pix.
= 780.16 Å		1.06 Å/pix.
x 736 pix.
= 780.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-36.441482999999998 - 62.330337999999998
Average (Standard dev.)0.17489964 (±3.7098813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-368-368-368
Dimensions736736736
Spacing736736736
CellA=B=C: 780.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_63001_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_63001_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 N4

EntireName: Escherichia phage N4 (virus)
Components
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: 32 kDa protein

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Supramolecule #1: Escherichia phage N4

SupramoleculeName: Escherichia phage N4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2886925 / Sci species name: Escherichia phage N4 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 44.074816 KDa
SequenceString: MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA ...String:
MLNYNAPTDG QKSSIDGANS DQMQTFFWLK KAIITARKEQ YFMPLASVTN MPKHYGKTIK VYEYVPLLDD RNINDQGIDA SGATIVNGN LYGSSKDIGN ITSKLPLLTE NGGRVNRVGF TRIAREGSIH KFGFFYEFTQ ESIDFDSDDG LMEHLSRELM N GATQITEA VLQKDLLAAA GTVLYAGAAT SDATITGEGS TPSVVSYKNL MRLDQILTEN RTPTQTTIIT GSRMIDTKVI GA TRVMYVG SELVPELKAM KDLFGNKAFI ETQHYADAGT IMNGEVGSID KFRIIQVPEM LHWAGAGAQA TGANPGYRTS MVS GQEHYD VYPMLVVGDD SFTSIGFQTD GKSLKFTVMT KMPGKETADR NDPYGETGFS SIKWYYGILV KRPERLALIK TVAP L

UniProtKB: Major capsid protein

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Macromolecule #2: 32 kDa protein

MacromoleculeName: 32 kDa protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 29.2059 KDa
SequenceString: MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV ...String:
MPVLKVMFHK DTNVATVLDA SGSLSDGSVE VGTFHHPDET YPDSVTIYHG VRDLLYKRSA KDPSQTASYP NNIINMQVIS IDMKATPRL ILGTALPRVI STIEGKDVTW HVDVAGGKAP LTYKWQFKAN TVGAAFADID SGENPTAKTA TLINHAVTAE S AGTYKVIV TDANGTTIES SSLLVVGVQE PPEVASIVAY PSPLALSVAD DITDGKTVKF SSLPAGSLIG TLSIKTQPDS GK ATAEISG NVLTVKPVAA GDTTVVVTNG TKEVTVTVNV TE

UniProtKB: 32 kDa protein

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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: 8
VitrificationCryogen name: ETHANE

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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: 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18940
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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