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- EMDB-36848: Structure of the bacteriophage lambda portal vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-36848
TitleStructure of the bacteriophage lambda portal vertex
Map data
Sample
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Portal protein B
KeywordsComplex / VIRAL PROTEIN
Function / homology
Function and homology information


viral portal complex / symbiont genome ejection through host cell envelope, long flexible tail mechanism / T=7 icosahedral viral capsid / virion assembly / viral capsid / host cell cytoplasm / structural molecule activity / DNA binding
Similarity search - Function
Phage portal protein, lambda family / Phage portal protein, lambda family / Major capsid protein GpE / Phage major capsid protein E
Similarity search - Domain/homology
Portal protein B / Major capsid protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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_36848.png

Downloads & links

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Map

FileDownload / File: emd_36848.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å		1.36 Å/pix.
x 400 pix.
= 544. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-28.270980000000002 - 43.077454000000003
Average (Standard dev.)0.0031920266 (±2.155182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36848_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36848_half_map_2.map
Projections & Slices
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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: Major capsid protein
    • Protein or peptide: Portal protein B

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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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 38.22916 KDa
SequenceString: MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT ...String:
MSMYTTAQLL AANEQKFKFD PLFLRLFFRE SYPFTTEKVY LSQIPGLVNM ALYVSPIVSG EVIRSRGGST SEFTPGYVKP KHEVNPQMT LRRLPDEDPQ NLADPAYRRR RIIMQNMRDE ELAIAQVEEM QAVSAVLKGK YTMTGEAFDP VEVDMGRSEE N NITQSGGT EWSKRDKSTY DPTDDIEAYA LNASGVVNII VFDPKGWALF RSFKAVKEKL DTRRGSNSEL ETAVKDLGKA VS YKGMYGD VAIVVYSGQY VENGVKKNFL PDNTMVLGNT QARGLRTYGC IQDADAQREG INASARYPKN WVTTGDPARE FTM IQSAPL MLLADPDEFV SVQLA

UniProtKB: Major capsid protein

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Macromolecule #2: Portal protein B

MacromoleculeName: Portal protein B / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 59.529609 KDa
SequenceString: MKTPTIPTLL GPDGMTSLRE YAGYHGGGSG FGGQLRSWNP PSESVDAALL PNFTRGNARA DDLVRNNGYA ANAIQLHQDH IVGSFFRLS HRPSWRYLGI GEEEARAFSR EVEAAWKEFA EDDCCCIDVE RKRTFTMMIR EGVAMHAFNG ELFVQATWDT S SSRLFRTQ ...String:
MKTPTIPTLL GPDGMTSLRE YAGYHGGGSG FGGQLRSWNP PSESVDAALL PNFTRGNARA DDLVRNNGYA ANAIQLHQDH IVGSFFRLS HRPSWRYLGI GEEEARAFSR EVEAAWKEFA EDDCCCIDVE RKRTFTMMIR EGVAMHAFNG ELFVQATWDT S SSRLFRTQ FRMVSPKRIS NPNNTGDSRN CRAGVQINDS GAALGYYVSE DGYPGWMPQK WTWIPRELPG GRASFIHVFE PV EDGQTRG ANVFYSVMEQ MKMLDTLQNT QLQSAIVKAM YAATIESELD TQSAMDFILG ANSQEQRERL TGWIGEIAAY YAA APVRLG GAKVPHLMPG DSLNLQTAQD TDNGYSVFEQ SLLRYIAAGL GVSYEQLSRN YAQMSYSTAR ASANESWAYF MGRR KFVAS RQASQMFLCW LEEAIVRRVV TLPSKARFSF QEARSAWGNC DWIGSGRMAI DGLKEVQEAV MLIEAGLSTY EKECA KRGD DYQEIFAQQV RETMERRAAG LKPPAWAAAA FESGLRQSTE EEKSDSRAA

UniProtKB: Portal protein B

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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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67924
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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