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- EMDB-47975: Cryo-EM structure of the portal-tail complex of LME-1 phage -

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Basic information

Entry
Database: EMDB / ID: EMD-47975
TitleCryo-EM structure of the portal-tail complex of LME-1 phage
Map dataunsharpened map
Sample
  • Virus: LME-1 (bacteria)
    • Protein or peptide: orf12
    • Protein or peptide: orf18
    • Protein or peptide: orf22
    • Protein or peptide: orf17
KeywordsLME-1 / legionella pneumophila / phage / portal / tail / podovirus / podophage / VIRAL PROTEIN
Function / homologyHead-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / symbiont entry into host cell / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria) / LME-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Phage resistance as an unexpected environmental determinant of the accidental virulence of Legionella pneumophila against the human host.
Authors: Nicholson B / Sante JF / Chaney EH / Deme JC / Deecker SR / Sztanko K / Davidson AR / Lea SM / Ensminger AW
History
DepositionNov 20, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47975.png

Downloads & links

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Map

FileDownload / File: emd_47975.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 800 pix.
= 702.4 Å		0.88 Å/pix.
x 800 pix.
= 702.4 Å		0.88 Å/pix.
x 800 pix.
= 702.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.4506554 - 1.3373338
Average (Standard dev.)-0.0018249414 (±0.03445716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 702.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47975_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: mask used for FSC calculation

Fileemd_47975_additional_1.map
Annotationmask used for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_47975_additional_2.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47975_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_47975_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LME-1

EntireName: LME-1 (bacteria)
Components
  • Virus: LME-1 (bacteria)
    • Protein or peptide: orf12
    • Protein or peptide: orf18
    • Protein or peptide: orf22
    • Protein or peptide: orf17

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Supramolecule #1: LME-1

SupramoleculeName: LME-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 446 / Sci species name: LME-1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: orf12

MacromoleculeName: orf12 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 62.743062 KDa
SequenceString: MVDVKKLLGK RDNSKLYEEI RKETKPKLDV NRLCRMRNDA KSDLDMWRSI LQTAYHYAMP DYNPFENYGL AGFLTPGQQY NADIYDLTL PIAHKRLADK MLMNMVPQGQ QWVKFTPGDE FGEPGTPLYQ RALDATQRMT DHFFKIIDRS NFYLAVGESL Q DVLISTGI ...String:
MVDVKKLLGK RDNSKLYEEI RKETKPKLDV NRLCRMRNDA KSDLDMWRSI LQTAYHYAMP DYNPFENYGL AGFLTPGQQY NADIYDLTL PIAHKRLADK MLMNMVPQGQ QWVKFTPGDE FGEPGTPLYQ RALDATQRMT DHFFKIIDRS NFYLAVGESL Q DVLISTGI IAINEGNRKR PVRYEAVPPA QVMFQGDAEG QVDAIFRDWY QVRIENIKSM WPKAEVAKLN KKPEDKVDIW EC AWIDYEA PEKERYQYVV MTSSKDVLLE QSNSSWPWVV YRMRRLTGEI RGRGPSLSAY PTAATINQAL EDELVAAAFQ ANP MYMAAS DSAFNQQTFT PRPGSIVPVQ MVQGEWPIKP FEQSGNIQFN ALLVNDFRQQ INELLYAFPL GAVNSPTRTA TEAE IRYTE NLESFSAMVP RLQNEFFIPV IQRTLWVINK VLPETFANIP DDIRNKMISV DGQILGLSFD TPLMTAKGQV KTAAL LGFY QAAASLLGPE AATASLDPVE VLTNLADNQG IDVRNIKTRE ELEQLLQAAG QIAQQEAAQQ GVIIGSEQPQ

UniProtKB: Uncharacterized protein

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Macromolecule #2: orf18

MacromoleculeName: orf18 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 89.921969 KDa
SequenceString: MPIRSISNTF NRGELDPTLF ARDDLDIYDK GARKLRNMIA LWTGAARIAP GTIYIDMMVD RENGNAVIQD PLMVKGFDFT YDADAEITY TIIIRKSGTN IAFDIYYADT LQTTVTSTAY LATQIQDIHV AAAHDRVLIL HENVQIRQLK RGASHSSWSL T TFNPRVYP ...String:
MPIRSISNTF NRGELDPTLF ARDDLDIYDK GARKLRNMIA LWTGAARIAP GTIYIDMMVD RENGNAVIQD PLMVKGFDFT YDADAEITY TIIIRKSGTN IAFDIYYADT LQTTVTSTAY LATQIQDIHV AAAHDRVLIL HENVQIRQLK RGASHSSWSL T TFNPRVYP TYDFSVIGEA INYQSFTFTL SATTGSITIT SSSAVFTHNH VGGLFRSLGG TARITAVAST TSASATVLDN FT GTSCAGN LSSLAEKLWN SDTTTAPVSA NRGWPARGVF YLNRLILGRS LAVKNLVNLS TAGVYDNFDD ADLDGLVAFS VTF NGKGEQ SVQSIVADDS ILFTTANKLF AQSPLVESPI TINNVYFAPQ SQSPATSIEA ASIDNQTLFV SSDRTKVMQA MYST ADGKY ITLPATMLSN SIVDYINSNG TWEPAGISTR LYLATQDNGT MLLYSTLQTQ NVAGWSLRTT TGKFRQVIGE GRQSH VIVE REINIGASFE QTLDYAYLSD PTFKARYDVT EFFASSPMTS AIGVLENQND YILIGNQAPF TALDIDFNLV ASSDCQ LQF EYLDGNGFWD VFTPTDNTSG FTVDGTITWT FDDVLNWAPY QVNAIENQYW IRIKRLAETV NTAPVIGQVL INTGNRI YL ERQSFDEYMD STQIVTSDSN GLVTGLTHLA GQQVYAITED GATIGSSFVD ASGETSVKNV NTTLTVGMQY KPELIPMP L YAPTQMGDSL YAEKYVQDLY VDYVDSLYLQ AGFRPQLTDI PNMHLGNYTL GQSVPPQTGI YRICPRGDWE PRQEFVITQ SQPGPMTIIG VGYNVEVA

UniProtKB: Uncharacterized protein

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Macromolecule #3: orf22

MacromoleculeName: orf22 / type: protein_or_peptide / ID: 3 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 68.819797 KDa
SequenceString: MSNIKINDVF QRIQYAASAG QTQFTIPFPF FDNEYVLVWQ NGVQLVMGGA PGQYGISGAG SPSGGLITLV TPAALNDIIT IQGDMPIDR TSIYSATISN LTGSDLNGDF NREVVMMKQI QTTQALLQLQ YAPWLEVSQD PDVTKDRYLP LLGSGQVWRM N DSGTGIEA ...String:
MSNIKINDVF QRIQYAASAG QTQFTIPFPF FDNEYVLVWQ NGVQLVMGGA PGQYGISGAG SPSGGLITLV TPAALNDIIT IQGDMPIDR TSIYSATISN LTGSDLNGDF NREVVMMKQI QTTQALLQLQ YAPWLEVSQD PDVTKDRYLP LLGSGQVWRM N DSGTGIEA YTIDETPAPS SSPFIIYQAD ATLSNAQNLG ALTSGILKQT VGGGSSTLSI AQNAVDYWAP GDELTRSQAP VS PDDVVNK AYADSIASGF TFINPVNAAS TANFNSTYNN GSSGVGATLT ATSNGAFSLD GQAGVLNKSY LMKDQTNTFE NGI YILTQV GDGSTPAILT RATYFDQPSE IQPGDLVPVL AGTVNNGTLW LQTDTVSAVG TDPITFIAFL PAFSNIVTIS GNQT ITGDK TFTGTTTLDN FIFVGSNIQH LGDTGNQIIF GTATQINTIN NNTISDLSSS GLRLGAANAR VSTILDEDDM ASDSA TALA TQQSIKAYVD NFRAAGAILQ TVSTNMTNTF SASLAAGSGF SDVTGFNVSI TPSATANKVF IKVDMLLASD TVDIVV VVR LKRNGTPIDI GNAAGSRIQI TTGSTNAKAL DGLQAVSFSF LDSPATTSAI TYQVDIGQRT SGSAVGIVVN RSGADVD SS SYTRGASTIT AQEIKG

UniProtKB: Uncharacterized protein

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Macromolecule #4: orf17

MacromoleculeName: orf17 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 22.792135 KDa
SequenceString: MIELTSAPTT KIEIISAAIS MVGKQQTVNT IDGGGALAID AEKLYDTLVS AELGSNRWRF AQAFQQISII TTLNPTFDGW LYECQIPAD CIMVQYLYPN IQYIVFGDKI LTKSNQTFTL IYSRNVPVSK WPPPFSLYIV YHLASMLGIS VTNSDRMLAR I SQGMEMWE ...String:
MIELTSAPTT KIEIISAAIS MVGKQQTVNT IDGGGALAID AEKLYDTLVS AELGSNRWRF AQAFQQISII TTLNPTFDGW LYECQIPAD CIMVQYLYPN IQYIVFGDKI LTKSNQTFTL IYSRNVPVSK WPPPFSLYIV YHLASMLGIS VTNSDRMLAR I SQGMEMWE SRALFADAQS SVTLPFRHNP YVDVRYRYKT RGY

UniProtKB: Uncharacterized 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 52.9 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: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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