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- EMDB-34250: Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor... -

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Basic information

Entry
Database: EMDB / ID: EMD-34250
TitleCryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex
Map data
SamplevB_DshS-R4C portal-adaptor complex != Dinoroseobacter phage vB_DshS-R4C

vB_DshS-R4C portal-adaptor complex

  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Head-to-tail joining protein
KeywordsMarine bacteriophage / Cryo-EM / Siphophage / Portal protein / Adaptor protein / Head-to-tail interface / VIRUS
Function / homologyPhage portal protein, lambda family / Phage portal protein, lambda family / virion assembly / structural molecule activity / Head-to-tail joining protein / Portal protein
Function and homology information
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHuang Y / Sun H / Wei S / Zheng Q / Li S / Zhang R / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structure and proposed DNA delivery mechanism of a marine roseophage.
Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng ...Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng / Shaowei Li / Rui Zhang / Ningshao Xia /
Abstract: Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene ...Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
History
DepositionSep 8, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34250.png

Downloads & links

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Map

FileDownload / File: emd_34250.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.128 Å
Density
Contour LevelBy EMDB: 0.0302
Minimum - Maximum-0.053432975 - 0.102033034
Average (Standard dev.)-0.00045212067 (±0.008139652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 270.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34250_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34250_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : vB_DshS-R4C portal-adaptor complex

EntireName: vB_DshS-R4C portal-adaptor complex
Components
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Head-to-tail joining protein

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Supramolecule #1: Dinoroseobacter phage vB_DshS-R4C

SupramoleculeName: Dinoroseobacter phage vB_DshS-R4C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2590919 / Sci species name: Dinoroseobacter phage vB_DshS-R4C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 60.353898 KDa
SequenceString: MRFWPFSKTT NAATRAEPMV TRPDTAPRVR SYRAAKSDRI AGGFGVFPTT PRDELRREIR GLVGHSRHAA QNFDYARAYE MLTRRHVIG FNGIRLQMDV RDPGGKKDVA AGAQIESAWA RWGKMKNSPT PCGRLSWWGV ECQVATGIAR EGGSFVRIHQ G TNRGRFGF ...String:
MRFWPFSKTT NAATRAEPMV TRPDTAPRVR SYRAAKSDRI AGGFGVFPTT PRDELRREIR GLVGHSRHAA QNFDYARAYE MLTRRHVIG FNGIRLQMDV RDPGGKKDVA AGAQIESAWA RWGKMKNSPT PCGRLSWWGV ECQVATGIAR EGGSFVRIHQ G TNRGRFGF QVEPIPFDLL DLDLTGPTPG GGFVGIAREG GSFVRIHQGT NRGRFGFQVE PIPFDLLDLD LTGPTPGGGF VE SGVEFDA TDRVVAYHMW SAAMSEGHRP GARRRLRIPA AQMLYVLVPE EIGQALGVPR SATALRLMNL SEKFQESALT AAN YGASNM VFFERAADNG VVTGPEDDAQ IPIDQIEAGT LTELPPGVKA VSHNPAYPDA AVGPFLRQMG TSQAAGLGVS YETL TADLS GANFSSLRAG KGEEREEWRM LQRAVFEGLH DRVFSRWLPL AMLSGEVRLP LAKLDKFDAA TWRPRGWPSV NPKDD ATAH EKDLKNGVRT RTEICAERGR DFADVVAEAA AERQMMRDAG LDPDAPLRTS PPETPPDPGE EIEGKDT

UniProtKB: Portal protein

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Macromolecule #2: Head-to-tail joining protein

MacromoleculeName: Head-to-tail joining protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 19.249615 KDa
SequenceString:
MTVSIHPPAT LVAGDSWAWE AGAVFEDHPD PWAASYVLRP EAGGDPVTVS GGLEVLAPVF RLPASVTADL PPGEWTWFAV AVDATTDAR AVLAQGRVTV IPDPLAGTED RRTPARRILA AIEATLEGRA TKDADTYSIE GRSITRTPLP DLLRLRAVYA E QVARETGR SPYRQRRVSF

UniProtKB: Head-to-tail joining protein

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 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: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: trRosetta server
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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