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- EMDB-47984: Cryo-EM structure of the icosahedral capsid of LME-1 phage -

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Basic information

Entry
Database: EMDB / ID: EMD-47984
TitleCryo-EM structure of the icosahedral capsid of LME-1 phage
Map dataunsharpened map used for model refinement
Sample
  • Virus: LME-1 (bacteria)
    • Protein or peptide: Phage major capsid protein
    • Protein or peptide: orf16
KeywordsLME-1 / phage / capsid / podovirus / podophage / VIRUS
Function / homologyPhage capsid protein / Phage capsid protein / Phage major capsid protein / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria) / LME-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 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-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47984.png

Downloads & links

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Map

FileDownload / File: emd_47984.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map used for model refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 1000 pix.
= 878. Å		0.88 Å/pix.
x 1000 pix.
= 878. Å		0.88 Å/pix.
x 1000 pix.
= 878. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.878 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.26191697 - 1.1082182
Average (Standard dev.)0.023968555 (±0.079001814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 878.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47984_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: mask used for FSC calculation

Fileemd_47984_additional_1.map
Annotationmask used for FSC calculation
Projections & Slices
AxesZYX

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Histogram

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Additional map: B-factor sharpened map

Fileemd_47984_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 1

Fileemd_47984_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47984_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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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: Phage major capsid protein
    • Protein or peptide: orf16

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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: Phage major capsid protein

MacromoleculeName: Phage major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 31.859764 KDa
SequenceString: MSLALSQIEI QQFLSEAHAE FQSEGFLLQG AVRTKSGTKG SIVHFPVFGE GMANQKAPQD DITPMNVSNR DAEAVIEDWY ASEYADRSF QNKLAVNAVE EYAKLCAWAI GRRADQINID TIAGATYSAT PNDQQGALVP VGTTGFTFEK LRQAHRWLRQ R SANRGKRT ...String:
MSLALSQIEI QQFLSEAHAE FQSEGFLLQG AVRTKSGTKG SIVHFPVFGE GMANQKAPQD DITPMNVSNR DAEAVIEDWY ASEYADRSF QNKLAVNAVE EYAKLCAWAI GRRADQINID TIAGATYSAT PNDQQGALVP VGTTGFTFEK LRQAHRWLRQ R SANRGKRT VIIDAIAEEQ LLNVEQLTNS FYVNQKILDN DGLHGMTFLG MNFIVIPSMQ EGGLPTTGGG TVGRAFFINE MA VGYAQSE RLGGDISWEN IKTSYLINMW MEAGAVVIDP KGLVEVDYLL EP

UniProtKB: Phage major capsid protein

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Macromolecule #2: orf16

MacromoleculeName: orf16 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 27.17648 KDa
SequenceString: MAFGINYMGR VSTSANNDTQ KVWIYNGTAT GSNETVATIA ASGYFNAFMV NVALGKGPLG VGDLIIINGN DASAFYTVQT ITPNVTVSV FAASGVVGTS NIQDGAVTAN KLATDSVTTV KILDDNVTSD KIAASVLKYV AVPLTAANII AMNGAPVQVL A AGGANTVH ...String:
MAFGINYMGR VSTSANNDTQ KVWIYNGTAT GSNETVATIA ASGYFNAFMV NVALGKGPLG VGDLIIINGN DASAFYTVQT ITPNVTVSV FAASGVVGTS NIQDGAVTAN KLATDSVTTV KILDDNVTSD KIAASVLKYV AVPLTAANII AMNGAPVQVL A AGGANTVH LVEHACLMMT YGTTQFTGGG AIGLQYGNTA ALAGEAASST IAAANVQGAA STMDMVEGAL SSGAFTAVAN LG LFISNNT AAFAAGDSDF VLHLWYRTVP TV

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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 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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