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- EMDB-38246: Closed state of central tail fiber of bacteriophage lambda -

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Basic information

Entry
Database: EMDB / ID: EMD-38246
TitleClosed state of central tail fiber of bacteriophage lambda
Map data
Sample
  • Complex: Bacteriophage lambda tail with LamB
    • Complex: tip attachment protein J
      • Protein or peptide: Tip attachment protein J
    • Complex: PPIA
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A
KeywordsBacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / periplasmic space ...symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / periplasmic space / 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 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Tip attachment protein J / Putative phage tail protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. ...Domain of unknown function DUF1983 / Domain of unknown function DUF3672 / : / Domain of unknown function (DUF1983) / Fibronectin type III protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Tip attachment protein J / Putative phage tail protein / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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 / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsGe XF / Wang JW
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371254 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural mechanism of bacteriophage lambda tail's interaction with the bacterial receptor.
Authors: Xiaofei Ge / Jiawei Wang /
Abstract: Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. ...Bacteriophage infection, a pivotal process in microbiology, initiates with the phage's tail recognizing and binding to the bacterial cell surface, which then mediates the injection of viral DNA. Although comprehensive studies on the interaction between bacteriophage lambda and its outer membrane receptor, LamB, have provided rich information about the system's biochemical properties, the precise molecular mechanism remains undetermined. This study revealed the high-resolution cryo-electron microscopy (cryo-EM) structures of the bacteriophage lambda tail complexed with its irreversible Shigella sonnei 3070 LamB receptor and the closed central tail fiber. These structures reveal the complex processes that trigger infection and demonstrate a substantial conformational change in the phage lambda tail tip upon LamB binding. Providing detailed structures of bacteriophage lambda infection initiation, this study contributes to the expanding knowledge of lambda-bacterial interaction, which holds significance in the fields of microbiology and therapeutic development.
History
DepositionDec 9, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38246.png

Downloads & links

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Map

FileDownload / File: emd_38246.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 480 pix.
= 497.28 Å		1.04 Å/pix.
x 480 pix.
= 497.28 Å		1.04 Å/pix.
x 480 pix.
= 497.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-3.649649 - 5.551311
Average (Standard dev.)-0.00011272188 (±0.052498914)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 497.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38246_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38246_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Bacteriophage lambda tail with LamB

EntireName: Bacteriophage lambda tail with LamB
Components
  • Complex: Bacteriophage lambda tail with LamB
    • Complex: tip attachment protein J
      • Protein or peptide: Tip attachment protein J
    • Complex: PPIA
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase A

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Supramolecule #1: Bacteriophage lambda tail with LamB

SupramoleculeName: Bacteriophage lambda tail with LamB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: tip attachment protein J

SupramoleculeName: tip attachment protein J / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia phage Lambda (virus)

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Supramolecule #3: PPIA

SupramoleculeName: PPIA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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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: 46.045844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: APAAPSRIEL TPGYFQITAT PHLAVYDPTV QFEFWFSEKQ IADIRQVETS TRYLGTALYW IAASINIKPG HDYYFYIRSV NTVGKSAFV EAVGRASDDA EGYLDFFKGK ITESHLGKEL LEKVELTEDN ASRLEEFSKE WKDASDKWNA MWAVKIEQTK D GKHYVAGI ...String:
APAAPSRIEL TPGYFQITAT PHLAVYDPTV QFEFWFSEKQ IADIRQVETS TRYLGTALYW IAASINIKPG HDYYFYIRSV NTVGKSAFV EAVGRASDDA EGYLDFFKGK ITESHLGKEL LEKVELTEDN ASRLEEFSKE WKDASDKWNA MWAVKIEQTK D GKHYVAGI GLSMEDTEEG KLSQFLVAAN RIAFIDPANG NETPMFVAQG NQIFMNDVFL KRLTAPTITS GGNPPAFSLT PD GKLTAKN ADISGSVNAN SGTLSNVTIA ENCTINGTLR AEKIVGDIVK AASAAFPRQR ESSVDWPSGT RTVTVTDDHP FDR QIVVLP LTFRGSKRTV SGRTTYSMCY LKVLMNGAVI YDGAANEAVQ VFSRIVDMPA GRGNVILTFT LTSTRHSADI PPYT FASDV QVMVIKKQAL GISVV

UniProtKB: Tip attachment protein J

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Macromolecule #2: Peptidyl-prolyl cis-trans isomerase A

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase A / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.453277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFKSTLAAMA AVFALSALSP AAMAAKGDPH VLLTTSAGNI ELELDKQKAP VSVQNFVDYV NSGFYNNTTF HRVIPGFMIQ GGGFTEQMQ QKKPNPPIKN EADNGLRNTR GTIAMARTAD KDSATSQFFI NVADNAFLDH GQRDFGYAVF GKVVKGMDVA D KISQVPTH DVGPYQNVPS KPVVILSAKV LP

UniProtKB: Peptidyl-prolyl cis-trans isomerase A

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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: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 369942
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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