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- EMDB-72881: N4 Empty Particle Portal -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-72881
TitleN4 Empty Particle Portal
Map data
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: 3.24 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) United States
CitationJournal: To Be Published
Title: Architecture of the giant RNA polymerase ejected from the coliphage N4 Capsid
Authors: Bellis NF / Lokareddy RK / Kizziah JL / Cooper SL / Schneider DA / Forti F / Briani F / Cingolani G
History
DepositionSep 25, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72881.png

Downloads & links

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Map

FileDownload / File: emd_72881.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.0467
Minimum - Maximum-0.18942755 - 0.3988697
Average (Standard dev.)0.0019335557 (±0.023357138)
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_72881_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72881_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72881_half_map_2.map
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: Yes
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 reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10265
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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