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- EMDB-54427: bacteriophage LUZ19 tail complex computed in C6 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-54427
Titlebacteriophage LUZ19 tail complex computed in C6 symmetry
Map dataC6 map
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Tail tubular protein B
    • Protein or peptide: Phage particle protein
    • Protein or peptide: tail channel protein
Keywordstail protein / tail fibres / genome delivery / STRUCTURAL PROTEIN
Function / homology: / Bacteriophage nozzle protein / Bacteriophage T7 tail fibre protein / Phage T7 tail fibre protein, N-terminal domain / virus tail / Uncharacterized protein gp29 / Tail tubular protein B / Phage particle protein
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsStefanik Sobotkova A / Cienikova Z / Mironova Y / Fuzik T / Plevka P / Hlavenkova Z / Novacek J
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 / Hlavenkova Z / Novacek J
History
DepositionJul 17, 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_54427.png

Downloads & links

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Map

FileDownload / File: emd_54427.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC6 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: 0.021
Minimum - Maximum-0.11070307 - 0.19833486
Average (Standard dev.)0.00037418585 (±0.0073664007)
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_54427_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C6 half1 map

Fileemd_54427_half_map_1.map
AnnotationC6 half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C6 half2 map

Fileemd_54427_half_map_2.map
AnnotationC6 half2 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: Tail tubular protein B
    • Protein or peptide: Phage particle protein
    • Protein or peptide: tail channel 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: 696 KDa

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Macromolecule #1: Tail tubular protein B

MacromoleculeName: Tail tubular protein B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 91.887297 KDa
SequenceString: SYKQSAYPNL LMGVSQQVPF ERLPGQLSEQ INMVSDPVSG LRRRSGIELM AHLLHTDQPW PRPFLYHTNL GGRSIAMLVA QHRGELYLF DERDGRLLMG QPLVHDYLKA NDYRQLRAAT VADDLFIANL SVKPEADRTD IKGVDPNKAG WLYIKAGQYS K AFSMTIKV ...String:
SYKQSAYPNL LMGVSQQVPF ERLPGQLSEQ INMVSDPVSG LRRRSGIELM AHLLHTDQPW PRPFLYHTNL GGRSIAMLVA QHRGELYLF DERDGRLLMG QPLVHDYLKA NDYRQLRAAT VADDLFIANL SVKPEADRTD IKGVDPNKAG WLYIKAGQYS K AFSMTIKV KDNATGTTYS HTATYVTPDN ASTNPNLAEA PFQTSVGYIA WQLYGKFFGA PEYTLPNSTK KYPKVDPDAN AA TIAGYLN QRGVQDGYIA FRGDADIHVE VSTDMGNNYG IASGGMSLNA TADLPALLPG AGAPGVGVQF MDGAVMATGS TKA PVYFEW DSANRRWAER AAYGTDWVLK KMPLALRWDE ATDTYSLNEL EYDRRGSGDE DTNPTFNFVT RGITGMTTFQ GRLV LLSQE YVCMSASNNP HRWFKKSAAA LNDDDPIEIA AQGSLTEPYE HAVTFNKDLI VFAKKYQAVV PGGGIVTPRT AVISI TTQY DLDTRAAPAV TGRSVYFAAE RALGFMGLHE MAPSPSTDSH YVAEDVTSHI PSYMPGPAEY IQAAASSGYL VFGTST ADE MICHQYLWQG NEKVQNAFHR WTLRHQIIGA YFTGDNLMVL IQKGQEIALG RMHLNSLPAR EGLQYPKYDY WRRIEAT VD GELELTKQHW DLIKDASAVY QLQPVAGAYM ERTHLGVKRE TNTKVFLDVP EAVVGAVYVV GCEFWSKVEF TPPVLRDH N GLPMTSTRAV LHRYNVNFGW TGEFLWRISD TARPNQPWYD TTPLRLFSRQ LNAGEPLVDS AVVPLPARVD MATSKFELS CHSPYDMNVR AVEYNFKSNQ TYRR

UniProtKB: Tail tubular protein B

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Macromolecule #2: Phage particle protein

MacromoleculeName: Phage particle protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 15.003919 KDa
SequenceString:
MARFKNPETI HVADGVEAVF SLDFPFLRRE DVFVQVDKIL VTDYTWVDDT NIQLAVVPKK DQEVRIFRDT PAQVPDTQFS QGIPFLPRY IDANNKQLLY AVQEGINTAN LALDGVLDAI RIAEEARRLA QEA

UniProtKB: Phage particle protein

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Macromolecule #3: tail channel protein

MacromoleculeName: tail channel protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 9.713819 KDa
SequenceString:
MLGKTIIGKL ADGLLGTDLS GAQSDARKME EQNRLMQQQA DQLARNQQVD LTAENVAQVD LGAMADATGT GTRRRRNQAG TGVSQTLGI NY

UniProtKB: Uncharacterized protein gp29

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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: 3.56 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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