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- EMDB-25675: Structure of bacteriophage lambda tube protein V in C3 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-25675
TitleStructure of bacteriophage lambda tube protein V in C3
Map dataBacteriophage lambda tube protein V in C3
Sample
  • Virus: Escherichia virus Lambda
    • Protein or peptide: Tail tube protein
KeywordsVirus / Phage / Lambda / Siphoviridae / Tail / Tube
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / host cell cytoplasm
Similarity search - Function
Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesEscherichia virus Lambda
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsProkhorov NS / Yang Q / Catalano CE / Morais MC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127365 United States
CitationJournal: To Be Published
Title: Structure of bacteriophage lambda tube protein V in C6
Authors: Prokhorov NS / Yang Q / Catalano CE / Morais MC
History
DepositionDec 9, 2021-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateJun 14, 2023-
Current statusJun 14, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25675.png

Downloads & links

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Map

FileDownload / File: emd_25675.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage lambda tube protein V in C3
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum-23.012284999999999 - 33.231506000000003
Average (Standard dev.)-0.000000000009538 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Bacteriophage lambda tube protein V in C3

Fileemd_25675_half_map_1.map
AnnotationBacteriophage lambda tube protein V in C3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacteriophage lambda tube protein V in C3

Fileemd_25675_half_map_2.map
AnnotationBacteriophage lambda tube protein V in C3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia virus Lambda

EntireName: Escherichia virus Lambda
Components
  • Virus: Escherichia virus Lambda
    • Protein or peptide: Tail tube protein

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Supramolecule #1: Escherichia virus Lambda

SupramoleculeName: Escherichia virus Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10710 / Sci species name: Escherichia virus Lambda / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia virus Lambda
Molecular weightTheoretical: 25.700582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PVPNPTMPVK GAGTTLWVYK GSGDPYANPL SDVDWSRLAK VKDLTPGELT AESYDDSYLD DEDADWTATG QGQKSAGDTS FTLAWMPGE QGQQALLAWF NEGDTRAYKI RFPNGTVDVF RGWVSSIGKA VTAKEVITRT VKVTNVGRPS MAEDRSTVTA A TGMTVTPA ...String:
PVPNPTMPVK GAGTTLWVYK GSGDPYANPL SDVDWSRLAK VKDLTPGELT AESYDDSYLD DEDADWTATG QGQKSAGDTS FTLAWMPGE QGQQALLAWF NEGDTRAYKI RFPNGTVDVF RGWVSSIGKA VTAKEVITRT VKVTNVGRPS MAEDRSTVTA A TGMTVTPA STSVVKGQST TLTVAFQPEG VTDKSFRAVS ADKTKATVSV SGMTITVNGV AAGKVNIPVV SGNGEFAAVA EI TVTAS

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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

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 653608
FSC plot (resolution estimation)

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