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- EMDB-54676: asymmetric unit of bacteriophage LUZ19 head computed in I4 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-54676
Titleasymmetric unit of bacteriophage LUZ19 head computed in I4 symmetry
Map datacapsid I4 map
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Particle protein
    • Protein or peptide: Minor structural protein
Keywordscapsid / head / icosahedron / bacteriophage / STRUCTURAL PROTEIN
Function / homologyParticle protein / Minor structural protein / Major capsid protein
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsStefanik Sobotkova A / Cienikova Z / Mironova Y / Fuzik T / Plevka P / Novacek J / Hlavenkova Z
Funding support Czech Republic, European Union, 2 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech Republic Czech Republic
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structure of bacteriophage LUZ19 native particle
Authors: Stefanik Sobotkova A / Cienikova Z / Mironova Y / Fuzik T / Plevka P / Novacek J / Hlavenkova Z
History
DepositionAug 6, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54676.png

Downloads & links

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Map

FileDownload / File: emd_54676.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcapsid I4 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 1000 pix.
= 1070. Å		1.07 Å/pix.
x 1000 pix.
= 1070. Å		1.07 Å/pix.
x 1000 pix.
= 1070. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0261
Minimum - Maximum-0.14968713 - 0.26093745
Average (Standard dev.)0.00038079295 (±0.008998346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1070.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: capsid I4 half2 map

Fileemd_54676_half_map_1.map
Annotationcapsid I4 half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: capsid I4 half1 map

Fileemd_54676_half_map_2.map
Annotationcapsid I4 half1 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 : Pseudomonas phage LUZ19

EntireName: Pseudomonas phage LUZ19 (virus)
Components
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Particle protein
    • Protein or peptide: Minor structural protein

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Supramolecule #1: Pseudomonas phage LUZ19

SupramoleculeName: Pseudomonas phage LUZ19 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 484896 / Sci species name: Pseudomonas phage LUZ19 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 324 KDa

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 37.760891 KDa
SequenceString: MSFLNDLTRP NYAGKNADVD IHLEEHLGIV DKHFAYTSKF APLMNIRDLR GSNVVRLDRL GNVEAKGRRA GEELERSRVV NDKWNLTVD TLLYLRHQFD HQDEWTQSFD MRKEVAELDG QELARKFDQA CLIQVIKAAA MDAPVDLEDA FSPGVLEKLD L TGLTAKQA ...String:
MSFLNDLTRP NYAGKNADVD IHLEEHLGIV DKHFAYTSKF APLMNIRDLR GSNVVRLDRL GNVEAKGRRA GEELERSRVV NDKWNLTVD TLLYLRHQFD HQDEWTQSFD MRKEVAELDG QELARKFDQA CLIQVIKAAA MDAPVDLEDA FSPGVLEKLD L TGLTAKQA ADKIVRMHRR VVETFIDRDL GDAVYSEGLT PMSPRVFSLL LEHDKLMNVE YQATGATNDY VKSRVAILNG VK VLETPRF ATKAIAAHPL GRHFNVSAEE SERQIALFLP SKTLITAQVA PVQAKLWEDN EKFSWVLDTF QMYNIGARRP DTA GAIELK GIGAFDITA

UniProtKB: Major capsid protein

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Macromolecule #2: Particle protein

MacromoleculeName: Particle protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 8.694855 KDa
SequenceString:
MATFAAATQK DLRAFAGTIE NLIRPLEEAA LGSGFTEVIT ITKDTDGNET RTSERKVRPE LVANLDALMA AVETAKAAVY K

UniProtKB: Particle protein

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Macromolecule #3: Minor structural protein

MacromoleculeName: Minor structural protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 10.574821 KDa
SequenceString:
MANTREQYLA GRNTGLTFYQ VCQPGTDNRI SLHDMDEADV KAKATAVIAA ATALGGEGGA TPPDPLTAYK VKNGDTLPVD GGGSVKVTV ANGAITKVVY TAPAG

UniProtKB: Minor structural 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: FEI FALCON III (4k x 4k) / Average electron dose: 94.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 51436
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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