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- EMDB-36677: AHS-CSF domains of phage lambda tail -

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Basic information

Entry
Database: EMDB / ID: EMD-36677
TitleAHS-CSF domains of phage lambda tail
Map data
Sample
  • Complex: bacteriophage lambda tail
    • Protein or peptide: Tip attachment protein J
KeywordsBacteriophage / caudovirales / siphoviridae / tail complex / delivery device / phage lambda / cryo-EM / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / virion attachment to host cell
Similarity search - Function
Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / Domain of unknown function (DUF1983) / Fibronectin type III protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Tip attachment protein J
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsWang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Structure / Year: 2024
Title: Architecture of the bacteriophage lambda tail.
Authors: Chang Wang / Jinsong Duan / Zhiwei Gu / Xiaofei Ge / Jianwei Zeng / Jiawei Wang /
Abstract: Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host ...Bacteriophage lambda has a double-stranded DNA genome and a long, flexible, non-contractile tail encoded by a contiguous block of 11 genes downstream of the head genes. The tail allows host recognition and delivery of viral DNA from the head shell to the cytoplasm of the infected cell. Here, we present a high-resolution structure of the tail complex of bacteriophage lambda determined by cryoelectron microscopy. Most component proteins of the lambda tail were determined at the atomic scale. The structure sheds light on the molecular organization of the extensively studied tail of bacteriophage lambda.
History
DepositionJun 28, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36677.png

Downloads & links

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Map

FileDownload / File: emd_36677.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.571043 - 4.3802066
Average (Standard dev.)-0.0031145648 (±0.020842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 429.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 1

Fileemd_36677_half_map_1.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_36677_half_map_2.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : bacteriophage lambda tail

EntireName: bacteriophage lambda tail
Components
  • Complex: bacteriophage lambda tail
    • Protein or peptide: Tip attachment protein J

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Supramolecule #1: bacteriophage lambda tail

SupramoleculeName: bacteriophage lambda tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage Lambda (virus)

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Macromolecule #1: Tip attachment protein J

MacromoleculeName: Tip attachment protein J / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 17.734773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ELLEKVELTE DNASRLEEFS KEWKDASDKW NAMAAVKAEQ TKDGKHYVAG IGLSMEDTEE GKLSQFLVAA NRIAAIDPAN GNETPMFVA QGNQIFMNDV FLKRLTAPTI TSGGNPPAFS LTPDGKLTAK NADISGSVNA NSGTLSNVTI AENCTINGTL R AEKIVG

UniProtKB: Tip attachment protein J

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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
VitrificationCryogen name: NITROGEN

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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: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233877
FSC plot (resolution estimation)

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