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- EMDB-72880: N4 Full Virion Portal -

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Basic information

Entry
Database: EMDB / ID: EMD-72880
TitleN4 Full Virion Portal
Map dataN4 Full Virion Portal
Sample
  • Virus: Escherichia phage N4 (virus)
    • Protein or peptide: Probable portal protein
Keywordsdodecamer / bacteriophage portal / 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 speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBellis NF / Cingolani G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
CitationJournal: Res Sq / Year: 2025
Title: Structure of the giant RNA polymerase ejected from coliphage N4.
Authors: Nathan F Bellis / Ravi K Lokareddy / Mikhail Pavlenok / Stephanie L Cooper Horton / James L Kizziah / Francesca Forti / David A Schneider / Michael Niederweis / Federica Briani / Gino Cingolani /
Abstract: are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two ... are widespread prokaryotic viruses that encapsidate a giant (~3,500-residue) virion-associated RNA polymerase (vRNAP). During infection, vRNAP is expelled into Gram-negative bacteria, along with two additional ejection proteins, to assemble a transient DNA-ejectosome that becomes transcriptionally active, initiating viral replication. Here, we present an integrative structural analysis of the coliphage N4 vRNAP (gp50). We find that this 383 kDa enzyme is a multi-domain, single-chain RNA polymerase, structurally distinct from both compact single-chain RNAPs and large multi-subunit holoenzymes. vRNAP is composed of loosely connected domains and exhibits an intramolecular mode of allosteric regulation through its C-terminal domain. Comparative analysis of intact and genome-released virions identified gp51, which forms an outer-membrane complex, and gp52, which assembles a periplasmic tunnel. These proteins generate heterogeneous pores that facilitate the release of vRNAP. We further uncover a signaling hub in the phage tail, composed of the receptor-binding protein, tail tube, and tail plug, that detects receptor engagement and orchestrates the release of ejection proteins. We propose that the beads-on-a-string architecture of vRNAP enables the translocation of megadalton-scale protein complexes through the ~35 Å channel formed by the tail and ejection proteins. These findings establish N4 as a distinctive model for protein translocation through biological channels.
History
DepositionSep 25, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72880.png

Downloads & links

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Map

FileDownload / File: emd_72880.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN4 Full Virion Portal
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 400 pix.
= 477.6 Å		1.19 Å/pix.
x 400 pix.
= 477.6 Å		1.19 Å/pix.
x 400 pix.
= 477.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.194 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.33797464 - 0.63634694
Average (Standard dev.)0.002158698 (±0.026436534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 477.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72880_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72880_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72880_half_map_2.map
AnnotationHalf Map A
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: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli str. K-12 substr. MG1655 (bacteria)

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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: Escherichia 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: 7
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 16320
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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