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- EMDB-36846: Structure of the bacteriophage lambda neck -

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Basic information

Entry
Database: EMDB / ID: EMD-36846
TitleStructure of the bacteriophage lambda neck
Map data
Sample
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail tube terminator protein
    • Protein or peptide: Head-tail connector protein FII
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / virion assembly / virion component / host cell cytoplasm
Similarity search - Function
Bacteriophage tail attachment protein FII / : / Phage Head-Tail Attachment protein / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) ...Bacteriophage tail attachment protein FII / : / Phage Head-Tail Attachment protein / Minor tail protein U-like / GpU-like superfamily / Phage minor tail protein U / Phage tail protein-like superfamily / 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
Head-tail connector protein FII / Tail tube terminator protein / Tail tube protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsXiao H / Tan L / Cheng LP / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: PLoS Biol / Year: 2023
Title: Structure of the siphophage neck-Tail complex suggests that conserved tail tip proteins facilitate receptor binding and tail assembly.
Authors: Hao Xiao / Le Tan / Zhixue Tan / Yewei Zhang / Wenyuan Chen / Xiaowu Li / Jingdong Song / Lingpeng Cheng / Hongrong Liu /
Abstract: Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; ...Siphophages have a long, flexible, and noncontractile tail that connects to the capsid through a neck. The phage tail is essential for host cell recognition and virus-host cell interactions; moreover, it serves as a channel for genome delivery during infection. However, the in situ high-resolution structure of the neck-tail complex of siphophages remains unknown. Here, we present the structure of the siphophage lambda "wild type," the most widely used, laboratory-adapted fiberless mutant. The neck-tail complex comprises a channel formed by stacked 12-fold and hexameric rings and a 3-fold symmetrical tip. The interactions among DNA and a total of 246 tail protein molecules forming the tail and neck have been characterized. Structural comparisons of the tail tips, the most diversified region across the lambda and other long-tailed phages or tail-like machines, suggest that their tail tip contains conserved domains, which facilitate tail assembly, receptor binding, cell adsorption, and DNA retaining/releasing. These domains are distributed in different tail tip proteins in different phages or tail-like machines. The side tail fibers are not required for the phage particle to orient itself vertically to the surface of the host cell during attachment.
History
DepositionJul 14, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36846.png

Downloads & links

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Map

FileDownload / File: emd_36846.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å		1.36 Å/pix.
x 360 pix.
= 489.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5
Minimum - Maximum-11.84632 - 22.07835
Average (Standard dev.)-0.0058157304 (±1.0799218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 489.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36846_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36846_half_map_2.map
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 phage Lambda

EntireName: Escherichia phage Lambda (virus)
Components
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Tail tube protein
    • Protein or peptide: Tail tube terminator protein
    • Protein or peptide: Head-tail connector protein FII

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Supramolecule #1: Escherichia phage Lambda

SupramoleculeName: Escherichia phage Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681611 / Sci species name: Escherichia phage Lambda / Virus type: VIRION / Virus isolate: SPECIES / 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 25.831779 KDa
SequenceString: MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ...String:
MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ASTSVVKGQS TTLTVAFQPE GVTDKSFRAV SADKTKATVS VSGMTITVNG VAAGKVNIPV VSGNGEFAAV AE ITVTAS

UniProtKB: Tail tube protein

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Macromolecule #2: Tail tube terminator protein

MacromoleculeName: Tail tube terminator protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 14.659124 KDa
SequenceString:
MKHTELRAAV LDALEKHDTG ATFFDGRPAV FDEADFPAVA VYLTGAEYTG EELDSDTWQA ELHIEVFLPA QVPDSELDAW MESRIYPVM SDIPALSDLI TSMVASGYDY RRDDDAGLWS SADLTYVITY EM

UniProtKB: Tail tube terminator protein

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Macromolecule #3: Head-tail connector protein FII

MacromoleculeName: Head-tail connector protein FII / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 12.775037 KDa
SequenceString:
MADFDNLFDA AIARADETIR GYMGTSATIT SGEQSGAVIR GVFDDPENIS YAGQGVRVEG SSPSLFVRTD EVRQLRRGDT LTIGEENFW VDRVSPDDGG SCHLWLGRGV PPAVNRRR

UniProtKB: Head-tail connector protein FII

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75098
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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