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- EMDB-62962: portal of mature phage N4 -

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Basic information

Entry
Database: EMDB / ID: EMD-62962
Titleportal of mature phage N4
Map dataportal of mature N4
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Probable portal protein
KeywordsComplex / VIRAL PROTEIN
Function / homology: / Phage SU10 portal protein / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / Probable portal protein
Function and homology information
Biological speciesEnterobacteria phage N4 (virus) / Escherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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 3, 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_62962.png

Downloads & links

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Map

FileDownload / File: emd_62962.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationportal of mature N4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 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: 2.0
Minimum - Maximum-5.827275 - 12.129166
Average (Standard dev.)0.00448889 (±0.6262127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map1

Fileemd_62962_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_62962_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: Probable portal 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: VIROID / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Probable portal protein

MacromoleculeName: Probable portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage N4 (virus)
Molecular weightTheoretical: 85.642523 KDa
SequenceString: MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF ...String:
MEQNTDSMVP LPDPSQATKL TSWKNELSLQ ALKADLDAAK PSHTAMMIKV KEWNDLMRIE GKAKPPKVKG RSQVQPKLVR RQAEWRYSA LTEPFLGSNK LFKVTPVTWE DVQGARQNEL VLNYQFRTKL NRVSFIDNYV RSVVDDGTGI VRVGWNREIR K EKQEVPVF SLFPIQTQEQ ADALQQALQL RTDNPRGYEE NVDEAIKESV RFFDETGQAT YAVQTGTTTT EVEVPLANHP TV EMLNPEN IIIDPSCQGD INKAMFAIVS FETCKADLLK EKDRYHNLNK IDWQSSAPVN EPDHATTTPQ EFQISDPMRK RVV AYEYWG FWDIEGNGVL EPIVATWIGS TLIRLEKNPY PDGKLPFVLI PYMPVKRDMY GEPDAELLGD NQAVLGAVMR GMID LLGRS ANGQRGMPKG MLDALNSRRY REGEDYEYNP TQNPAQMIIE HKFPELPQSA LTMATLQNQE AESLTGVKAF AGGVT GESY GDVAAGIRGV LDAASKREMA ILRRLAKGMS EIGNKIIAMN AVFLAEHEVV RITNEEFVTI KREDLKGNFD LEVDIS TAE VDNQKSQDLG FMLQTIGPNV DQQITLNILA EIADLKRMPK LAHDLRTWQP QPDPVQEQLK QLAVEKAQLE NEELRSK IR LNDAQAQKAM AERDNKNLDY LEQESGTKHA RDLEKMKAQS QGNQQLEITK ALTKPRKEGE LPPNLSAAIG YNALTNGE D TGIQSVSERD IAAEANPAYS LGSSQFDPTR DPALNPGIRL GN

UniProtKB: Probable portal 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47179
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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