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- EMDB-75838: N4 Periplasmic Tunnel Fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-75838
TitleN4 Periplasmic Tunnel Fragment
Map data
Sample
  • Complex: N4 Periplasmic Tunnel Fragment
    • Protein or peptide: 66 kDa protein
KeywordsBacteriophage / Ejection Protein / Membrane Channel / VIRAL PROTEIN
Function / homology66 kDa protein
Function and homology information
Biological speciesEscherichia phage N4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBellis NF / Lokareddy RK / Cingolani G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140733 United States
National Institutes of Health/Office of the DirectorOD024978 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
DepositionMar 5, 2026-
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_75838.png

Downloads & links

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Map

FileDownload / File: emd_75838.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 600 pix.
= 429.54 Å		0.72 Å/pix.
x 600 pix.
= 429.54 Å		0.72 Å/pix.
x 600 pix.
= 429.54 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7159 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00926
Minimum - Maximum-0.067031145 - 0.18745583
Average (Standard dev.)0.000025984908 (±0.0030855704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 429.54 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75838_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75838_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_75838_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 : N4 Periplasmic Tunnel Fragment

EntireName: N4 Periplasmic Tunnel Fragment
Components
  • Complex: N4 Periplasmic Tunnel Fragment
    • Protein or peptide: 66 kDa protein

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Supramolecule #1: N4 Periplasmic Tunnel Fragment

SupramoleculeName: N4 Periplasmic Tunnel Fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage N4 (virus)

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Macromolecule #1: 66 kDa protein

MacromoleculeName: 66 kDa protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage N4 (virus)
Molecular weightTheoretical: 38.738797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAQITWRNVD APSFSGVGDS IRTFSNMLGN ATAGLSNALG DFRNSARQQA GDAIMAEAMR YQDPNEYRNA LASGALFAGY DPSLISSRT MENLDNRAGN LLDQASKQQN LDFTRYSNDR TMKVNAATDA AAPALQELAL AYQSGDPRKV QAAQAQYGDV L KTLPAGIV ...String:
MAQITWRNVD APSFSGVGDS IRTFSNMLGN ATAGLSNALG DFRNSARQQA GDAIMAEAMR YQDPNEYRNA LASGALFAGY DPSLISSRT MENLDNRAGN LLDQASKQQN LDFTRYSNDR TMKVNAATDA AAPALQELAL AYQSGDPRKV QAAQAQYGDV L KTLPAGIV MDYMNNLQGQ GTAGIGQRRS LFNLGVDMRN DADTQAAMQL LNNIRRGAYS SDDARMLAEG TFDQMSPGAV SR ALSQLDR AYPGAYTPGT GSAPLSPPGT HGTRNGSAYD TTYKFTPTDV PITQMNLGEV VQHQDTMKKT LGASPVGAYQ INQ DTLKDF APKVFGENWQ NIPMSPENQD KLGEAIFNAR KNG

UniProtKB: 66 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: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS F200C
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold 3
Final reconstructionApplied symmetry - Point group: C10 (10 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 77357
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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