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- EMDB-35826: Tail fiber of phage lambda tail -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-35826
TitleTail fiber of phage lambda tail
Map data
Sample
  • Complex: Tail tip conformation 1 of phage lambda tail
    • Protein or peptide: gpJ
KeywordsBacteriophage / caudovirales / siphoviridae / tail complex / delivery device / macromolecular assembly / 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 DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / : / : / Tip attachment protein J,FNIII-A domain / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein ...Domain of unknown function DUF3672 / : / Tip attachment protein J, C-terminal receptor binding domain / Tip attachment protein J, Ig-like domain / Tip attachment protein J second Ig-like domain / : / : / Tip attachment protein J,FNIII-A domain / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber 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: 6.07 Å
AuthorsWang JW / Wang C
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
DepositionApr 5, 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_35826.png

Downloads & links

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Map

FileDownload / File: emd_35826.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å		1.07 Å/pix.
x 400 pix.
= 429.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.365
Minimum - Maximum-0.9498841 - 1.9078748
Average (Standard dev.)-0.0023901486 (±0.033707995)
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 map

Fileemd_35826_half_map_1.map
Annotationhalf 1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half 2 map

Fileemd_35826_half_map_2.map
Annotationhalf 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 : Tail tip conformation 1 of phage lambda tail

EntireName: Tail tip conformation 1 of phage lambda tail
Components
  • Complex: Tail tip conformation 1 of phage lambda tail
    • Protein or peptide: gpJ

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Supramolecule #1: Tail tip conformation 1 of phage lambda tail

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

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Macromolecule #1: gpJ

MacromoleculeName: gpJ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
SequenceString: MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETVL GTEVKYDTPI TRTITSANID RLRFTFGVQA LVETTSKGDR NPSEVRLLVQ IQRNGGWVTE KDITIKGKTT SQYLASVVMG ...String:
MGKGSSKGHT PREAKDNLKS TQLLSVIDAI SEGPIEGPVD GLKSVLLNST PVLDTEGNTN ISGVTVVFRA GEQEQTPPEG FESSGSETVL GTEVKYDTPI TRTITSANID RLRFTFGVQA LVETTSKGDR NPSEVRLLVQ IQRNGGWVTE KDITIKGKTT SQYLASVVMG NLPPRPFNIR MRRMTPDSTT DQLQNKTLWS SYTEIIDVKQ CYPNTALVGV QVDSEQFGSQ QVSRNYHLRG RILQVPSNYN PQTRQYSGIW DGTFKPAYSN NMAWCLWDML THPRYGMGKR LGAADVDKWA LYVIGQYCDQ SVPDGFGGTE PRITCNAYLT TQRKAWDVLS DFCSAMRCMP VWNGQTLTFV QDRPSDKTWT YNRSNVVMPD DGAPFRYSFS ALKDRHNAVE VNWIDPNNGW ETATELVEDT QAIARYGRNV TKMDAFGCTS RGQAHRAGLW LIKTELLETQ TVDFSVGAEG LRHVPGDVIE ICDDDYAGIS TGGRVLAVNS QTRTLTLDRE ITLPSSGTAL ISLVDGSGNP VSVEVQSVTD GVKVKVSRVP DGVAEYSVWE LKLPTLRQRL FRCVSIREND DGTYAITAVQ HVPEKEAIVD NGAHFDGEQS GTVNGVTPPA VQHLTAEVTA DSGEYQVLAR WDTPKVVKGV SFLLRLTVTA DDGSERLVST ARTTETTYRF TQLALGNYRL TVRAVNAWGQ QGDPASVSFR IAAPAAPSRI ELTPGYFQIT ATPHLAVYDP TVQFEFWFSE KQIADIRQVE TSTRYLGTAL YWIAASINIK PGHDYYFYIR SVNTVGKSAF VEAVGRASDD AEGYLDFFKG KITESHLGKE LLEKVELTED NASRLEEFSK EWKDASDKWN AMWAVKIEQT KDGKHYVAGI GLSMEDTEEG KLSQFLVAAN RIAFIDPANG NETPMFVAQG NQIFMNDVFL KRLTAPTITS GGNPPAFSLT PDGKLTAKNA DISGSVNANS GTLSNVTIAE NCTINGTLRA EKIVGDIVKA ASAAFPRQRE SSVDWPSGTR TVTVTDDHPF DRQIVVLPLT FRGSKRTVSG RTTYSMCYLK VLMNGAVIYD GAANEAVQVF SRIVDMPAGR GNVILTFTLT STRHSADIPP YTFASDVQVM VIKKQALGIS VV

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: 7.5
VitrificationCryogen name: NITROGEN

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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: 2.0 µm / Nominal defocus min: 1.0 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: 6.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28128
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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