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- EMDB-38245: Open State of central tail fiber of bacteriophage lambda upon bin... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38245
TitleOpen State of central tail fiber of bacteriophage lambda upon binding to LamB (gpJ713-LamB complex)
Map data
Sample
  • Complex: Bacteriophage lambda tail with LamB
    • Complex: LamB
      • Protein or peptide: Maltoporin
    • Complex: Tip attachment protein J
      • Protein or peptide: Tip attachment protein J
KeywordsBacteriophage / caudovirales / siphoviridae / phage lambda / host recognition / LamB / cryo-EM / VIRUS
Function / homology
Function and homology information


maltodextrin transmembrane transporter activity / maltose transporting porin activity / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / pore complex / monoatomic ion transport / cell outer membrane / host cell cytoplasm / entry receptor-mediated virion attachment to host cell ...maltodextrin transmembrane transporter activity / maltose transporting porin activity / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / pore complex / monoatomic ion transport / cell outer membrane / 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
Maltoporin / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / 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 ...Maltoporin / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / 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
Maltoporin / Tip attachment protein J
Similarity search - Component
Biological speciesShigella sonnei (bacteria) / Escherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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: To Be Published
Title: Cryo-EM structure of lambda tail with LamB
Authors: Ge XF / Wang JW
History
DepositionDec 9, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38245.png

Downloads & links

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Map

FileDownload / File: emd_38245.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0742 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.228786 - 4.061357
Average (Standard dev.)0.001964488 (±0.087997764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 386.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38245_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_38245_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 : Bacteriophage lambda tail with LamB

EntireName: Bacteriophage lambda tail with LamB
Components
  • Complex: Bacteriophage lambda tail with LamB
    • Complex: LamB
      • Protein or peptide: Maltoporin
    • Complex: Tip attachment protein J
      • Protein or peptide: Tip attachment protein J

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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: LamB

SupramoleculeName: LamB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Shigella sonnei (bacteria)

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Supramolecule #3: Tip attachment protein J

SupramoleculeName: Tip attachment protein J / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia phage Lambda (virus)

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Macromolecule #1: Maltoporin

MacromoleculeName: Maltoporin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Shigella sonnei (bacteria)
Molecular weightTheoretical: 47.568004 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVDFHGYARS GIGWTGSGGE QQCFQTTGAQ SKYRLGNECE TYAELKLGQE VWKEGDKSFY FDTNVAYSVA QQNDWEATDP AFREANVQG KNLIEWLPGS TIWAGKRFYQ RHDVHMIDFY YWDISGPGAG LENIDVGFGK LSLAATRSSE AGGSSSFASN N IYDYTNET ...String:
AVDFHGYARS GIGWTGSGGE QQCFQTTGAQ SKYRLGNECE TYAELKLGQE VWKEGDKSFY FDTNVAYSVA QQNDWEATDP AFREANVQG KNLIEWLPGS TIWAGKRFYQ RHDVHMIDFY YWDISGPGAG LENIDVGFGK LSLAATRSSE AGGSSSFASN N IYDYTNET ANDVFDVRLA QMEINPGGTL ELGVDYGRAN LRDNYRLVDG ASKDGWLFTA EHTQSVLKGF NKFVVQYATD SM TSQGKGL SQGSGVAFDN EKFAYNINNN GHMLRILDHG AISMGDNWDM MYVGMYQDIN WDNDNGTKWW TVGIRPMYKW TPI MSTVME IGYDNVESQR TGDKNNQYKI TLAQQWQAGD SIWSRPAIRV FATYAKWDEK WGYDYNGDSK VNPNYGKAVP ADFN GGSFG RGDSDEWTFG AQMEIWW

UniProtKB: Maltoporin

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Macromolecule #2: Tip attachment protein J

MacromoleculeName: Tip attachment protein J / type: protein_or_peptide / ID: 2 / 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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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 621549
FSC plot (resolution estimation)

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