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- EMDB-64745: C12 portal complex of the bacteriophage E1004 -

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Basic information

Entry
Database: EMDB / ID: EMD-64745
TitleC12 portal complex of the bacteriophage E1004
Map data
Sample
  • Complex: Escherichia phage
    • Protein or peptide: Portal protein
KeywordsComplex / Viral protein
Function / homologyPortal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEscherichia phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsSun BN / Liu HR
Funding support China, 3 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
CitationJournal: To Be Published
Title: C12 portal complex of the bacteriophage E1004
Authors: Sun BN / Liu HR
History
DepositionMay 21, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64745.png

Downloads & links

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Map

FileDownload / File: emd_64745.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.84055203 - 1.4142532
Average (Standard dev.)0.0010172278 (±0.07182403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64745_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_64745_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

EntireName: Escherichia phage (virus)
Components
  • Complex: Escherichia phage
    • Protein or peptide: Portal protein

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Supramolecule #1: Escherichia phage

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

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1
Details: The sequence of organism Saccharomyces cerevisiae is not available during the biocuration, replaced by A0A1S6KVI5 temporarily.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 57.330652 KDa
SequenceString: MAEREGFAAE GAKAVYDRLK NGRQPYETRA QNCAAVTIPS LFPKESDNSS TEYTTPWQAV GARCLNNLAA KLMLALFPQS PWMRLTVSE YEAKTLSQDS EAAARVDEGL AMVERVLMAY METNSFRVPL FEALKQLIVS GNCLLYIPEP EQGTYSPMRM Y RLVSYVVQ ...String:
MAEREGFAAE GAKAVYDRLK NGRQPYETRA QNCAAVTIPS LFPKESDNSS TEYTTPWQAV GARCLNNLAA KLMLALFPQS PWMRLTVSE YEAKTLSQDS EAAARVDEGL AMVERVLMAY METNSFRVPL FEALKQLIVS GNCLLYIPEP EQGTYSPMRM Y RLVSYVVQ RDAFGNILQI VTLDKVAFSA LPEDVKSQLN ADDYEPDTEL EVYTHIYRQD DEYLRYEEVE GIEVAGTEGS YP LTACPYI PVRMVRLDGE DYGRSYCEEY LGDLNSLETI TEAITKMAKV ASKVVGLVNP NGITQPRRLN KAATGEFVAG RVE DINFLQ LTKGQDFTIA KSVADAIEQR LGWAFLLNSA VQRNAERVTA EEIRYVAGEL EATLGGVYSV QSQELQLPIV RVLM NQLQS AGMIPDLPKE AVEPTVSTGL EALGRGQDLE KLTQAVNMMT GLQPLSQDPD INLPTLKLRL LNALGIDTAG LLLTQ DEKI QRMAEQSSQQ AVVQGASAAG ANMGAAVGQG AGEDMAQA

UniProtKB: 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.2 µm / Nominal defocus min: 1.6 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54423
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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