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- EMDB-55352: Special vertex of bacteriophage LUZ19 computed in C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-55352
TitleSpecial vertex of bacteriophage LUZ19 computed in C1 symmetry
Map dataspecial vertex C1 masked map
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Tail tubular protein A
    • Protein or peptide: Head-tail connector protein
Keywordsspecial vertex / portal / adaptor / capsid / connector / STRUCTURAL PROTEIN
Function / homologyTail tubular protein Gp11 / Tail tubular protein / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / Head-tail connector protein / Major capsid protein / Tail tubular protein A
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.01 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
DepositionOct 14, 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_55352.png

Downloads & links

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Map

FileDownload / File: emd_55352.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationspecial vertex C1 masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 Å		1.07 Å/pix.
x 416 pix.
= 445.12 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: 0.0195
Minimum - Maximum-0.08763325 - 0.123998895
Average (Standard dev.)0.00017116888 (±0.006292829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 445.12003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55352_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: special vertex C1 half2 map

Fileemd_55352_half_map_1.map
Annotationspecial vertex C1 half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: special vertex C1 half1 map

Fileemd_55352_half_map_2.map
Annotationspecial vertex C1 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: Tail tubular protein A
    • Protein or peptide: Head-tail connector 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: 1.494 MDa

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 15 / 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: Tail tubular protein A

MacromoleculeName: Tail tubular protein A / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 21.211096 KDa
SequenceString:
MLLLDAVNVI LRKIGELPIP SMDETYPTMA IALPELEDQR IQLLTQGWWF NTWWRHKLTP DPTGRINLPK GTLAFYPDSP DLQWDGLGV RDANTGDDRI GKPVEGRLVL SREWDHIPEI AQRVIAHQAA LAVYTHEIGP DETAQVIAQE LQAYQNELSR M HTRSRPLN TQAKRSFSRW RRSLRT

UniProtKB: Tail tubular protein A

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Macromolecule #3: Head-tail connector protein

MacromoleculeName: Head-tail connector protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 56.169305 KDa
SequenceString: MKTTAAMLWE KLRDGSVESR AIEFAKTTLP YLMVDPMSGS RGVVEHDFQS AGALLVNNLA AKLARSLFPT GIPFFRSELT DAIRREADS RDTDITEVTA ALARVDRKAT QRLFQNASLA VLTQVIKLLI VTGNALLYRD SAAATVVAWS LRSYAVRRDA T GRWMDIVL ...String:
MKTTAAMLWE KLRDGSVESR AIEFAKTTLP YLMVDPMSGS RGVVEHDFQS AGALLVNNLA AKLARSLFPT GIPFFRSELT DAIRREADS RDTDITEVTA ALARVDRKAT QRLFQNASLA VLTQVIKLLI VTGNALLYRD SAAATVVAWS LRSYAVRRDA T GRWMDIVL KQRYKSKDLD EEYKQDLMRA GRNLSGSGSV DLYTHVQRKK GTAMEYAELY HEIDGVRVGK EGRWPIHLCP YI VPTWNLA PGEHYGRGHV EDYIGDFAKL SLLSEKLGLY ELESLEVLNL VDEAKGAVVD DYQDAEMGDY VPGGAEAVRA YER GDYNKM AAIQQSLQAV VVRLNQAFMY GANQRDAERV TAEEVRITAE EAENTLGGTY SLLAENLQSP LAYVCLSEVD DALL QGLIT KQHKPAIETG LPALSRSAAV QSMLNASQVI AGLAPIAQLD PRISLPKMMD TIWAAFSVDT SQFYKSADEL EAEAE QQRQ QAAQAQAAQE TLLEGASDMT NALAGV

UniProtKB: Head-tail connector 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: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 21683
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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