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- EMDB-34249: Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail... -

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Basic information

Entry
Database: EMDB / ID: EMD-34249
TitleCryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex
Map data
Sample
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Major tail protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Megatron protein
    • Protein or peptide: Hub protein
    • Protein or peptide: Ribonuclease III
KeywordsMarine bacteriophage / Cryo-EM / Siphophage / Baseplate / Megatron protein / Tail fibre protein / Distal tail protein / Hub protein / VIRAL PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 ...Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Gene transfer agent / Ribonuclease III / Tail protein / Tail protein / Major tail protein
Similarity search - Component
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34249.png

Downloads & links

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Map

FileDownload / File: emd_34249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.40361714 - 1.7806563
Average (Standard dev.)0.00070497795 (±0.08194961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34249_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_34249_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 : Dinoroseobacter phage vB_DshS-R4C

EntireName: Dinoroseobacter phage vB_DshS-R4C (virus)
Components
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
    • Protein or peptide: Major tail protein
    • Protein or peptide: Distal tail protein
    • Protein or peptide: Megatron protein
    • Protein or peptide: Hub protein
    • Protein or peptide: Ribonuclease III

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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: Major tail protein

MacromoleculeName: Major tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 13.574816 KDa
SequenceString:
MLKGKDGVVK NASTGDSIGH LQSWALDTQR DEVSGWGMGD DAERAFTTVG RASGNFEVYL DPADPSDDLE PGDLVDLELY PGGESTGSG YRSVAGALIL STAESASKDG IPMLTVNWRT SGALPQKATV S

UniProtKB: Major tail protein

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Macromolecule #2: Distal tail protein

MacromoleculeName: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 23.378309 KDa
SequenceString: MQFIDVEFPR DIAAGCQAVL TRRDEVVTLA SGREEVNSRW ADTRRSWDAG LGVRDEADLA QVVALFEEVR GRLYAFRFRD WLDWRTAAT RAPITATDQP LGLGDGSRTA FQVVKVYGAV NPYTRPLSLP HPGTVRVALD GVTQPSGWTL TAPGGVITFD T PPALGVTV ...String:
MQFIDVEFPR DIAAGCQAVL TRRDEVVTLA SGREEVNSRW ADTRRSWDAG LGVRDEADLA QVVALFEEVR GRLYAFRFRD WLDWRTAAT RAPITATDQP LGLGDGSRTA FQVVKVYGAV NPYTRPLSLP HPGTVRVALD GVTQPSGWTL TAPGGVITFD T PPALGVTV TAGCSFDVPV RFSDPELAVQ WAYFREGQAG LAQAPSIPLI EVRLDP

UniProtKB: Tail protein

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Macromolecule #3: Megatron protein

MacromoleculeName: Megatron protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 154.569125 KDa
SequenceString: MATVLLAAAG GAIGTSLGGA LFGISAAVIG QAVGGLIGQT IDARLSGGGT IKQTGPRLDS LEVMVSQEGT PLADISGRVA VAGTVIWAT KLEEIARTTS TRVGSGKSSQ KVKSTNFDYA ASFAVSLGEG PLNGIGRIFL DGQVRDLSEM ISENRVRFYP G TEDQEPDP ...String:
MATVLLAAAG GAIGTSLGGA LFGISAAVIG QAVGGLIGQT IDARLSGGGT IKQTGPRLDS LEVMVSQEGT PLADISGRVA VAGTVIWAT KLEEIARTTS TRVGSGKSSQ KVKSTNFDYA ASFAVSLGEG PLNGIGRIFL DGQVRDLSEM ISENRVRFYP G TEDQEPDP LIEAIEGAAP AFRGTAYLVF ERLFLSDFGN RVPQVRVEVF GQSGEMEKGV TGVCVIPGST EFGYMPAPVR QQ SLDGADV VWEGPENCNR YSRISDWSLS MDHLKNTLPA VQTVSLVVAW FGTDLRAGLC RFEPRIELRA KRTSIEWIAA GLN RGSATE VSRDENDRPA FGSSPADVSV VRAIMDLKAR GFRVVLYPFV MMDVTADQAL PSPAGTGAQG AYPWRGRIMP DVTG GRVSD QIAALMGTAQ PDDFTAAVTR NKSGEISQVN LTCPGAPGDA GLRRFILHLA KLADIAGGVD AFLVGTEFRG LSQAW EPQT YADAYEFLNS SEGWFAQNAA RTHEPGSLLV SATARDPRLI SPPLSIDGAA ARWIEIEFDR TSAPVWEGNV YYMTED HGF AGAFRKVISD AEAPADGTRA RMLLDMHDLT LGGDDWRTST ITRLRFDFSS ESDAVFRIHA IRLGGGRRYP FVDALRD LA QDVDTILPTA KISYAADWSE YHSHQDAGDL TFHLDPLWAD PAIDFVGIDN YLPLSDWRQG ADHLDYDATS GRTTPYDL D YLKSNIEGGE YWDWFYASQE DRDTQTRTPI SDGSYGEPWV FRQKAIRDWH ANAHHNRTAG VRATTSTGWV PGSKPVWFT EYGCPAVDLG ANRPNVFAAA SSSESALPWY SSGLRDDFMQ RQYLRAMAEW WTANGAPAVD LANCQAWAWD ARPFPEFPLR PATWSDGPD WRLGHWLNGR AGAAPAAEAI TRRAITRHGL ISADIDTSRA YGQADGYAAP APLGLGDYAQ PFEVALGLQT T ETGGALVI EAKPAAPLAA DVIEADLVDT PAIYTLTRGA LEDTPAAAIV RFRDGLSDYE ITAARARIGA GKEGGSATAD LA LVLDGDR GNAAAEMVLR AALTSRESLS VTLPRSATTL RPGSLVEVTL GTEARRLFLV DRVVDGQARE VTLRGFDRAA YAP SGGVFK AARAGRLQGS TSSLTRFLDL PLLPGVDAPE WEGFIAAHAE PWPGAMLHSR GSTPEGSFTL AAEADARATI GRTT AALPP APAHVWTPGP LVVTLFSGAL VGRPDLDVLD GANALAIQHP DGWEVVQFRE ATLTADRTWR LEGLLRGQRG TDGIV GPAP LPAGAAVVAI DTALVAAGLS ADDPGRALWW RSGPDAASLA AAPLRPHTFT AAGLRAFPPA HLRAVVTGGG DTSLSW VPR SRLVGTTWPD NGAPIPSGEG LERYQVTIGP TAAPVRVILA DTPAATYTAA ERAADGIAAP FRVAVSQISE TTGPGPW IE TIVTE

UniProtKB: Tail protein

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Macromolecule #4: Hub protein

MacromoleculeName: Hub protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 31.055357 KDa
SequenceString: MTDYTDHLAT GCTTLARCYI LTRRDGVVMG FTDHDRDIDL DGTRCAAGAA LDASTAARSL GITPDDMDAG GALSADAITE ADLRAGRYD GAQVEVWEVN WTDPAVRGRL GVYTIGQVER GPLAFRAELR TRPALWNRPE GRIHTALCDV DRLGDHRCKL A LGPWQSAA ...String:
MTDYTDHLAT GCTTLARCYI LTRRDGVVMG FTDHDRDIDL DGTRCAAGAA LDASTAARSL GITPDDMDAG GALSADAITE ADLRAGRYD GAQVEVWEVN WTDPAVRGRL GVYTIGQVER GPLAFRAELR TRPALWNRPE GRIHTALCDV DRLGDHRCKL A LGPWQSAA TVIEADGADL IVSGLDETAS NIFDRGVLDW TGGANAGTGS DIRVARPVAG GVRVSLWSAP PFPITAGDTA NA TVGCDRT ADTCRNRFDN LANFRGFPLM PGESFISEYA RPGDPDQSGG SRYD

UniProtKB: Gene transfer agent

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Macromolecule #5: Ribonuclease III

MacromoleculeName: Ribonuclease III / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Molecular weightTheoretical: 22.783799 KDa
SequenceString: MPTPFLALPL IAEGQAGQHV THNEALDMID ALAPRVVLSD SLATPPPAPP DRSAWIVPPG GSGFGGAGPG QIALRLGGVW HAITPAQGA RWRVLDRGAA VIWSGTSWRP ADVSGALGST LGLATIEATV TATGPSVTAP ALIPPRAIVL GVTSWTVQAV T GATSYRVG ...String:
MPTPFLALPL IAEGQAGQHV THNEALDMID ALAPRVVLSD SLATPPPAPP DRSAWIVPPG GSGFGGAGPG QIALRLGGVW HAITPAQGA RWRVLDRGAA VIWSGTSWRP ADVSGALGST LGLATIEATV TATGPSVTAP ALIPPRAIVL GVTSWTVQAV T GATSYRVG VPGEPDKFGA SLGAAPGSSN IGVVGPFATY APTDVVVTAE GADFTGGTIG LAASVILPGA PV

UniProtKB: Ribonuclease III

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: trRosetta server
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11598

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