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- EMDB-38556: Mature virion portal of phage lambda with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-38556
TitleMature virion portal of phage lambda with DNA
Map data
Sample
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Head-tail connector protein FII
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail tube terminator protein
    • Protein or peptide: Portal protein B
    • Protein or peptide: Tail tube protein
    • DNA: DNA (104-MER)
    • DNA: DNA (92-MER)
KeywordsBacteriophage / caudovirales / siphoviridae / portal vertex / portal / capsid / connector/neck / tail / delivery device / B-DNA / VIRAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


virus tail, tube / viral portal complex / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / virion assembly / viral life cycle / virion component / host cell cytoplasm / structural molecule activity / DNA binding
Similarity search - Function
Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / : / Head-to-tail joining protein W / Minor tail protein U-like / Head-to-tail joining protein W superfamily / GpU-like superfamily / gpW / Phage minor tail protein U / Phage tail protein-like superfamily ...Bacteriophage tail attachment protein FII / Phage Head-Tail Attachment / : / Head-to-tail joining protein W / Minor tail protein U-like / Head-to-tail joining protein W superfamily / GpU-like superfamily / gpW / Phage minor tail protein U / Phage tail protein-like superfamily / Phage portal protein, lambda family / Phage portal protein, lambda family / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Portal protein B / Head-tail connector protein FII / Tail tube terminator protein / Tail tube protein / Head completion protein
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 4, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38556.png

Downloads & links

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Map

FileDownload / File: emd_38556.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.)
1.07 Å/pix.
x 480 pix.
= 515.616 Å		1.07 Å/pix.
x 480 pix.
= 515.616 Å		1.07 Å/pix.
x 480 pix.
= 515.616 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: 0.52
Minimum - Maximum-1.3849941 - 2.199375
Average (Standard dev.)-0.016078925 (±0.1423847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 515.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38556_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_38556_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 : Escherichia phage Lambda

EntireName: Escherichia phage Lambda (virus)
Components
  • Virus: Escherichia phage Lambda (virus)
    • Protein or peptide: Head-tail connector protein FII
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail tube terminator protein
    • Protein or peptide: Portal protein B
    • Protein or peptide: Tail tube protein
    • DNA: DNA (104-MER)
    • DNA: DNA (92-MER)

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Supramolecule #1: Escherichia phage Lambda

SupramoleculeName: Escherichia phage Lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #7, #4, #3, #1-#2, #5-#6 / NCBI-ID: 2681611 / Sci species name: Escherichia phage Lambda / Virus type: VIRION / Virus isolate: SEROCOMPLEX / Virus enveloped: No / Virus empty: No

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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
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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Macromolecule #2: Tail tube protein

MacromoleculeName: Tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 25.831779 KDa
SequenceString: MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ...String:
MPVPNPTMPV KGAGTTLWVY KGSGDPYANP LSDVDWSRLA KVKDLTPGEL TAESYDDSYL DDEDADWTAT GQGQKSAGDT SFTLAWMPG EQGQQALLAW FNEGDTRAYK IRFPNGTVDV FRGWVSSIGK AVTAKEVITR TVKVTNVGRP SMAEDRSTVT A ATGMTVTP ASTSVVKGQS TTLTVAFQPE GVTDKSFRAV SADKTKATVS VSGMTITVNG VAAGKVNIPV VSGNGEFAAV AE ITVTAS

UniProtKB: Tail tube protein

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Macromolecule #3: Tail tube terminator protein

MacromoleculeName: Tail tube terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 14.659124 KDa
SequenceString:
MKHTELRAAV LDALEKHDTG ATFFDGRPAV FDEADFPAVA VYLTGAEYTG EELDSDTWQA ELHIEVFLPA QVPDSELDAW MESRIYPVM SDIPALSDLI TSMVASGYDY RRDDDAGLWS SADLTYVITY EM

UniProtKB: Tail tube terminator protein

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Macromolecule #4: Head completion protein

MacromoleculeName: Head completion protein / type: protein_or_peptide / ID: 4 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 7.625749 KDa
SequenceString:
MTRQEELAAA RAALHDLMTG KRVATVQKDG RRVEFTATSV SDLKKYIAEL EVQTGMTQRR RGPAGFYV

UniProtKB: Head completion protein

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Macromolecule #7: Head-tail connector protein FII

MacromoleculeName: Head-tail connector protein FII / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 12.775037 KDa
SequenceString:
MADFDNLFDA AIARADETIR GYMGTSATIT SGEQSGAVIR GVFDDPENIS YAGQGVRVEG SSPSLFVRTD EVRQLRRGDT LTIGEENFW VDRVSPDDGG SCHLWLGRGV PPAVNRRR

UniProtKB: Head-tail connector protein FII

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Macromolecule #5: DNA (104-MER)

MacromoleculeName: DNA (104-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 32.0115 KDa
SequenceString: (DC)(DT)(DG)(DC)(DA)(DC)(DC)(DA)(DA)(DA) (DC)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DG) (DT)(DG)(DC)(DG)(DT)(DG)(DC)(DA)(DA) (DC)(DA)(DC)(DT)(DA)(DT)(DA)(DC)(DA)(DT) (DC) (DT)(DA)(DC)(DT)(DA)(DT) ...String:
(DC)(DT)(DG)(DC)(DA)(DC)(DC)(DA)(DA)(DA) (DC)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DG)(DG) (DT)(DG)(DC)(DG)(DT)(DG)(DC)(DA)(DA) (DC)(DA)(DC)(DT)(DA)(DT)(DA)(DC)(DA)(DT) (DC) (DT)(DA)(DC)(DT)(DA)(DT)(DT)(DA) (DG)(DT)(DA)(DA)(DT)(DA)(DG)(DT)(DG)(DA) (DA)(DA) (DT)(DG)(DC)(DC)(DC)(DA)(DG) (DG)(DA)(DA)(DA)(DG)(DG)(DC)(DC)(DA)(DC) (DT)(DA)(DG) (DG)(DC)(DT)(DG)(DT)(DC) (DC)(DA)(DA)(DT)(DG)(DC)(DC)(DC)(DC)(DG) (DC)(DC)(DG)(DC) (DT)(DG)(DG)(DA)

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Macromolecule #6: DNA (92-MER)

MacromoleculeName: DNA (92-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 28.412127 KDa
SequenceString: (DG)(DC)(DA)(DT)(DT)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DC)(DT)(DA)(DG)(DT)(DG)(DG)(DC) (DC)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DG) (DG)(DC)(DA)(DT)(DT)(DT)(DC)(DA)(DC)(DT) (DA) (DT)(DT)(DA)(DC)(DT)(DA) ...String:
(DG)(DC)(DA)(DT)(DT)(DG)(DG)(DA)(DC)(DA) (DG)(DC)(DC)(DT)(DA)(DG)(DT)(DG)(DG)(DC) (DC)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DG) (DG)(DC)(DA)(DT)(DT)(DT)(DC)(DA)(DC)(DT) (DA) (DT)(DT)(DA)(DC)(DT)(DA)(DA)(DT) (DA)(DG)(DT)(DA)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA) (DG)(DT)(DG)(DT)(DT)(DG)(DC) (DA)(DC)(DG)(DC)(DA)(DC)(DC)(DT)(DC)(DC) (DG)(DG)(DT) (DA)(DG)(DT)(DT)(DT)(DG) (DG)(DT)(DG)(DC)(DA)(DG)

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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19060
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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