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- EMDB-38540: Prohead portal of bacteriophage lambda -

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Basic information

Entry
Database: EMDB / ID: EMD-38540
TitleProhead portal of bacteriophage lambda
Map data
Sample
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Portal protein B
Keywordscaudovirales / siphoviridae / portal vertex / portal / capsid / connector/neck / tail / delivery device / B-DNA / VIRAL PROTEIN
Function / homologyPhage portal protein, lambda family / Phage portal protein, lambda family / viral portal complex / symbiont genome ejection through host cell envelope, long flexible tail mechanism / virion assembly / structural molecule activity / DNA binding / Portal protein B
Function and homology information
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsWang JW / Gu ZW
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: J Virol / Year: 2024
Title: Structural morphing in the viral portal vertex of bacteriophage lambda.
Authors: Zhiwei Gu / Kexun Wu / Jiawei Wang /
Abstract: The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA ...The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system.
IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple ...IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.
History
DepositionJan 2, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38540.png

Downloads & links

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Map

FileDownload / File: emd_38540.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 256 pix.
= 334.474 Å		1.31 Å/pix.
x 256 pix.
= 334.474 Å		1.31 Å/pix.
x 256 pix.
= 334.474 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.582011 - 1.1203306
Average (Standard dev.)0.0026244456 (±0.080548935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 334.47424 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38540_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_38540_half_map_2.map
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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: 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: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Portal protein B

MacromoleculeName: Portal protein B / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 59.529609 KDa
Recombinant expressionOrganism: Escherichia phage Lambda (virus)
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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50921
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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