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- EMDB-56773: portal - core interface of bacteriophage LUZ19 computed in C4 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-56773
Titleportal - core interface of bacteriophage LUZ19 computed in C4 symmetry
Map dataportal middle core map in C4 symmetry
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Head-tail connector protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: UNK
    • Protein or peptide: UNK
Keywordscore / portal / ejectosome / connector / STRUCTURAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope / symbiont genome ejection through host cell envelope, short tail mechanism / virion component / lysozyme activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Internal virion protein Gp14 / T7 virus internal virion protein gp14 family / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Head-tail connector protein / Internal virion protein / Internal virion protein
Similarity search - Component
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.83 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
DepositionFeb 17, 2026-
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_56773.png

Downloads & links

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Map

FileDownload / File: emd_56773.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationportal middle core map in C4 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 Å		1.07 Å/pix.
x 480 pix.
= 513.6 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: 0.0139
Minimum - Maximum-0.06460015 - 0.115950115
Average (Standard dev.)0.00017943564 (±0.003388013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 513.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56773_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: portal middle core half1 map in C4 symmetry

Fileemd_56773_half_map_1.map
Annotationportal middle core half1 map in C4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: portal middle core half2 map in C4 symmetry

Fileemd_56773_half_map_2.map
Annotationportal middle core half2 map in C4 symmetry
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: Head-tail connector protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: Internal virion protein
    • Protein or peptide: UNK
    • Protein or peptide: UNK

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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: 402 KDa

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Macromolecule #1: Head-tail connector protein

MacromoleculeName: Head-tail connector protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / 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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Macromolecule #2: Internal virion protein

MacromoleculeName: Internal virion protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 18.852318 KDa
SequenceString:
MAFWLPLLAA GGMSALQQGL ANKEERNKIK AENKARLKTD LDNLGAAARD IANLGVMAAS YRKQAVASQV EAKRQGMLAG GSAEAQAGA FGVKGASVDA VALDIEREVG EALIQIDDNL DNQMWNLAEQ AHSIQAQAKA GLLGQKSTTA GQRSPLVAGL M SAGSLYAS QYFKFGATPK GGN

UniProtKB: Internal virion protein

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Macromolecule #3: Internal virion protein

MacromoleculeName: Internal virion protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 98.368633 KDa
SequenceString: MAESQRASQE LGINVGQTQL QPGQSARRGV RDSEINYSGP SVGSQILDGI LGAGQQIAGK WFEHNVQQEV LRGERARMAG EAEEAVDSN VLAKPFVKGG WRKQDYRIAQ ADFSLKMQRF IANKGREMTP EEFRKYLSQE ATHVLDSTEG MNPNDALQAL A QQQKAEEQ ...String:
MAESQRASQE LGINVGQTQL QPGQSARRGV RDSEINYSGP SVGSQILDGI LGAGQQIAGK WFEHNVQQEV LRGERARMAG EAEEAVDSN VLAKPFVKGG WRKQDYRIAQ ADFSLKMQRF IANKGREMTP EEFRKYLSQE ATHVLDSTEG MNPNDALQAL A QQQKAEEQ LFGMQAKAYM DWSIDQAARG FRTQGNSILA KAVQAQATGD ELSRQLSLEE AGLFYTNIMT SEDIPLEVRD KV GMQFLAA SLDMNQRGIY EGLRDAGFLD SMSFDDRRAL NGLYEKSKAQ TRAKESMATL RADADFQQRV ANGAITDLAE VEA YSRGMV EEGRWSDAQA ISFMTKAMTG LGNAQRMQGI MAALEAGDIN ALHTLGTNVT EALEQWDKMQ AANGSSLTDR LVQG TQLGL RLGTFPKTYG ESVGSAVRMI QAAKEGEANP ELVNTLNSIF EQVASAQEIN PSAGNVMLSG IPEAEQGAVA WALKQ MKMG IAPAQALREF SANAEVVKQM DEFEKGQNTK AFKDNLGKQV NDKFVNNIFG RAWNMLTGES DLSNNEAVLS MYRRAT IDE ANWLASDRKH AGLLTSDTGR EALLEIAAAN VRNRTIQVGE GRNLKEGDLF SRRDSAPLIL PRGTTAEQLF GTNDTET IG TVLAEQHKPH VEGLLGYKSV VAFEYDRTSG SLLAVEYDEN GVALDRTRVD PQAVGNEVLK RNADKLNAMR GAEYGANV K ISGTDIRMNG GNSAGMLKQD VFNWRKELAQ FEAYRGEAYK DADGYSVGLG HYLGSGNAGA GTTVTPEQAA QWFAEDTDR ALDQGVRLAD ELGVTNNASI LGLAGMAFQM GEGRARQFRN TFQAIKDRNK EAFEAGVRNS KWYTQTPNRA EAFIKRMAPH FDTPSQIGV DWYSAATAE

UniProtKB: Internal virion protein

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Macromolecule #4: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 1.635006 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #5: UNK

MacromoleculeName: UNK / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 1.890321 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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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: 3.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 18360
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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