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Yorodumi- EMDB-34250: Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34250 | |||||||||
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Title | Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex | |||||||||
Map data | ||||||||||
Sample | vB_DshS-R4C portal-adaptor complex != Dinoroseobacter phage vB_DshS-R4C vB_DshS-R4C portal-adaptor complex
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Keywords | Marine bacteriophage / Cryo-EM / Siphophage / Portal protein / Adaptor protein / Head-to-tail interface / VIRUS | |||||||||
Function / homology | Phage 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 species | Dinoroseobacter phage vB_DshS-R4C (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.7 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_34250.map.gz | 49.2 MB | EMDB map data format | |
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Header (meta data) | emd-34250-v30.xml emd-34250.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_34250.png | 102 KB | ||
Filedesc metadata | emd-34250.cif.gz | 5.5 KB | ||
Others | emd_34250_half_map_1.map.gz emd_34250_half_map_2.map.gz | 36.9 MB 36.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34250 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34250 | HTTPS FTP |
-Validation report
Summary document | emd_34250_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_34250_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_34250_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_34250_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34250 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34250 | HTTPS FTP |
-Related structure data
Related structure data | 8gtdMC 8gtaC 8gtbC 8gtcC 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_34250.map.gz / Format: CCP4 / Size: 52.7 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: 1.128 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34250_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34250_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : vB_DshS-R4C portal-adaptor complex
Entire | Name: vB_DshS-R4C portal-adaptor complex |
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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: Portal protein
Macromolecule | Name: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 60.353898 KDa |
Sequence | String: 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 |
-Macromolecule #2: Head-to-tail joining protein
Macromolecule | Name: Head-to-tail joining protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Molecular weight | Theoretical: 19.249615 KDa |
Sequence | String: 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 |
-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: 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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |