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Yorodumi- EMDB-34249: Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34249 | |||||||||
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Title | Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Marine 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, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal ...Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily Similarity search - Domain/homology | |||||||||
Biological species | Dinoroseobacter phage vB_DshS-R4C (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Huang Y / Sun H / Wei S / Zheng Q / Li S / Zhang R / Xia N | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34249.map.gz | 229.9 MB | EMDB map data format | |
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Header (meta data) | emd-34249-v30.xml emd-34249.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_34249.png | 39.1 KB | ||
Filedesc metadata | emd-34249.cif.gz | 6.9 KB | ||
Others | emd_34249_half_map_1.map.gz emd_34249_half_map_2.map.gz | 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34249 | HTTPS FTP |
-Validation report
Summary document | emd_34249_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34249_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34249_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_34249_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34249 | HTTPS FTP |
-Related structure data
Related structure data | 8gtcMC 8gtaC 8gtbC 8gtdC 8gtfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34249.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34249_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34249_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dinoroseobacter phage vB_DshS-R4C
Entire | Name: Dinoroseobacter phage vB_DshS-R4C (virus) |
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Components |
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-Supramolecule #1: Dinoroseobacter phage vB_DshS-R4C
Supramolecule | Name: 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 |
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Host (natural) | Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria) |
-Macromolecule #1: Major tail protein
Macromolecule | Name: Major tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 13.574816 KDa |
Sequence | String: MLKGKDGVVK NASTGDSIGH LQSWALDTQR DEVSGWGMGD DAERAFTTVG RASGNFEVYL DPADPSDDLE PGDLVDLELY PGGESTGSG YRSVAGALIL STAESASKDG IPMLTVNWRT SGALPQKATV S UniProtKB: Major tail protein |
-Macromolecule #2: Distal tail protein
Macromolecule | Name: Distal tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 23.378309 KDa |
Sequence | String: 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 |
-Macromolecule #3: Megatron protein
Macromolecule | Name: Megatron protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 154.569125 KDa |
Sequence | String: 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 |
-Macromolecule #4: Hub protein
Macromolecule | Name: Hub protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 31.055357 KDa |
Sequence | String: 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 |
-Macromolecule #5: Ribonuclease III
Macromolecule | Name: Ribonuclease III / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 22.783799 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: OTHER / Details: trRosetta server |
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Final reconstruction | Applied 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 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |