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- EMDB-54828: cap and middle core protein of bacteriophage LUZ19 computed in C4... -

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Basic information

Entry
Database: EMDB / ID: EMD-54828
Titlecap and middle core protein of bacteriophage LUZ19 computed in C4 symmetry
Map datacore complex masked map in C4 symmetry
Sample
  • Virus: Pseudomonas phage LUZ19 (virus)
    • Protein or peptide: Internal virion protein
    • Protein or peptide: Internal virion protein
Keywordscap protein / middle core protein / core / ejectosome / STRUCTURAL PROTEIN
Function / homologyLysozyme domain superfamily / lysozyme activity / Lysozyme-like domain superfamily / killing of cells of another organism / defense response to bacterium / Internal virion protein / Internal virion protein
Function and homology information
Biological speciesPseudomonas phage LUZ19 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 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 20, 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_54828.png

Downloads & links

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Map

FileDownload / File: emd_54828.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcore complex masked 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: 0.0134
Minimum - Maximum-0.052752316 - 0.08846979
Average (Standard dev.)0.00007559163 (±0.0025552846)
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_54828_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: core complex half1 map in C4 symmetry

Fileemd_54828_half_map_1.map
Annotationcore complex half1 map in C4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: core complex half2 map in C4 symmetry

Fileemd_54828_half_map_2.map
Annotationcore complex 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: Internal virion protein
    • Protein or peptide: Internal virion 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: 1.36 MDa

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Macromolecule #1: Internal virion protein

MacromoleculeName: Internal virion protein / type: protein_or_peptide / ID: 1 / 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 #2: Internal virion protein

MacromoleculeName: Internal virion protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage LUZ19 (virus)
Molecular weightTheoretical: 144.220312 KDa
SequenceString: MAKQFKGRMT PKYPLDQAQL DEAQVQGQLD AVPTVGFDAL TGGEIGERNV AAGQRANARE LERIVADQEL PALDRASALW NQSTLVGRW GDALQLDADL AANSTGEVDP NFDAGTYGVQ ALQAAGIQPT DNYLQIMARA GNAEDAAYLL SRIQRYEQDE Q VVRDNPYW ...String:
MAKQFKGRMT PKYPLDQAQL DEAQVQGQLD AVPTVGFDAL TGGEIGERNV AAGQRANARE LERIVADQEL PALDRASALW NQSTLVGRW GDALQLDADL AANSTGEVDP NFDAGTYGVQ ALQAAGIQPT DNYLQIMARA GNAEDAAYLL SRIQRYEQDE Q VVRDNPYW NFAAGMLDPA ALAVDAVTFG AGRALRLGRA GMAAAGGAGQ VGYVAGLDAA GADVDAGTYI VAGALGAGVG AL LGSGAGR IAAEAPTQPH VPEVSAPTVG LPEVAMTTEE AAARGFKAGD VVDLLDEGTV LSRVSAKVEQ AEIPAIPRRD TAF GDELHS LSGRKLSEVL DHLKTHAEVP KPLQGIAAKV ADTIRTLESL GQRTAFRVVQ GGDTASSAFL KPGTAGIHST QGLD TLVQV RGSTAPGRVG TNPVTVLHEA VHAATVGVMN AALRNPGAMS PKVAQAMQTL ENVRGNVLNA LKQDRAAGRQ LSEFE ETLL AGNSNTLANV KELVAWGLTD TRFQRTLNRL RYSDGGPGLW SRFVEGIRTL LGLRSDADTA LSRVLAASET IMEAMP GYT KAQAKWANKG APVTEEASLE TIVRSTRERA REGAGFVNRF FSEADLLAQP GEGARRLLSR LIDDPVRRDG FSTNDNA AS YLRRYRNEFE GYVKSYDEMM AKAMAEQGVG LTARALNSRR AMAVRDQLNE QVTRELLRRD REWTAYGSVR VDPNLPPT I KALADRSDEI HGLMGQRARE AGVRGFENFA PRPGYFHRSW NWSKMAQMDE AAPGLARRAI SEAVFRGIPG LERADADTI AQAIVQRARD RATGIRSEFM GAMGVADTAF IRQALEEANV SQAKFDSIMA KIEQKQSDQG TVKYGKGRLS LDMTAEINHN GTVYRVQDL IDRDLDRLME NYAGSMSGRS ALARAGMPGD SEIEAFIREY QREAAHLGTD KVQELTGQLR GVFGDFTGNV P REHQLGPV AQRASGLTSA TMLGFSGVYQ LAELATMAHR QGVFNVMKAM LNSRLGDFVG AMRRDPDLAD EMQTVLGLNL AN DIRMKPW KRQFDTFLAS QDTFMDRFLH AGKQAVPVLN GMKFIHNWQS RMNANLTLNK VARAAQGDEA ALRVLQQYGK DVD WTPVLA RVRGYVTYRG RNAQSMNWGA WSQADVNTVM NTALRIMDDS LLYGRVGQNS GFARSPVGQI LGQFRSFVAF AHNK LLRGT YENSGVLGVA SLLAFQYPLT ALMMGAKAAI NGKFDTSDEG IRKMAIDGIG YTAGLGFTAD MWGVITGHSR MSAPV FGLA EHSNEVFRGV KDLVTGDDPA AATGDIVNGA AGALPFVNVF PATKLLLESI KGE

UniProtKB: Internal virion 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: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17830
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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