+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34539 | |||||||||||||||
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Title | Capsid structure of Ralstonia phage GP4 | |||||||||||||||
Map data | capsid | |||||||||||||||
Sample |
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Keywords | Ralstonia phage GP4 / Complex / VIRUS | |||||||||||||||
Function / homology | Protein of unknown function DUF4043 / Protein of unknown function (DUF4043) / Virion associated protein / Major capsid protein Function and homology information | |||||||||||||||
Biological species | Ralstonia phage GP4 (virus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Liu HR / Chen WY | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Viruses / Year: 2022 Title: A Capsid Structure of GP4 with a Triangulation Number T = 9. Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Xiaowu Li / Jingdong Song / Lingpeng Cheng / Hongrong Liu / Abstract: GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo- ...GP4, a new phage, is a short-tailed phage. Few structures of phages have been resolved to near-atomic resolution until now. Here, we present a 3.7 Å resolution structure of the GP4 head by cryo-electron microscopy (cryo-EM). The GP4 head contains 540 copies of major capsid protein (MCP) gp2 and 540 copies of cement protein (CP) gp1 arranged in an icosahedral shell with a triangulation number T = 9. The structures of gp2 and gp1 show a canonical HK97-like fold and an Ig-like fold, respectively. The trimeric CPs stick on the surface of the head along the quasi-threefold axis of the icosahedron generating a sandwiched three-layer electrostatic complementary potential, thereby enhancing the head stability. The assembly pattern of the GP4 head provides a platform for the further exploration of the interaction between and corresponding phages. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34539.map.gz | 858.7 MB | EMDB map data format | |
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Header (meta data) | emd-34539-v30.xml emd-34539.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_34539.png | 144.7 KB | ||
Others | emd_34539_half_map_1.map.gz emd_34539_half_map_2.map.gz | 225.6 MB 225.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34539 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34539 | HTTPS FTP |
-Validation report
Summary document | emd_34539_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_34539_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_34539_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | emd_34539_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34539 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34539 | HTTPS FTP |
-Related structure data
Related structure data | 8h89MC 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_34539.map.gz / Format: CCP4 / Size: 926.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | capsid | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.27 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1
File | emd_34539_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_34539_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ralstonia phage GP4
Entire | Name: Ralstonia phage GP4 (virus) |
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Components |
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-Supramolecule #1: Ralstonia phage GP4
Supramolecule | Name: Ralstonia phage GP4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2282904 / Sci species name: Ralstonia phage GP4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Ralstonia phage GP4 (virus) |
Molecular weight | Theoretical: 40.819551 KDa |
Sequence | String: MSSTVIAFGD PKAQKKWSSE LAVDIRKKSY FESRFIGTSE NAVIQRKTEV ESDAGDRVSF DLSVRLRGQP TFGDDRVEGK EENLKFYTD EVIIDQVRHS VSAGGRMSRK RTAHDLRKTG RDRLGDYFYQ LTDELFFMYL SGARGINKDF ILPTSFTGYA K NPFNTPDA ...String: MSSTVIAFGD PKAQKKWSSE LAVDIRKKSY FESRFIGTSE NAVIQRKTEV ESDAGDRVSF DLSVRLRGQP TFGDDRVEGK EENLKFYTD EVIIDQVRHS VSAGGRMSRK RTAHDLRKTG RDRLGDYFYQ LTDELFFMYL SGARGINKDF ILPTSFTGYA K NPFNTPDA AHLLYGGVAT SKASLANTDT MSRVVIERAN VQATMMQAQD PETANMVPVS VEGEDRYVCV MSPFQEHSLR TS DAAGWLE IQKAAAAAEG RNNPIFKGGL GMIGNTVLHS HRNVVRFSDY GAGSDQPAAR ALFMGRQAAV VAYGTKGGLR YDW QEETKD YGNEPTVASG FIAGIKKTRF NDRDFGVISI DTYAKDPNPN NPA UniProtKB: Major capsid protein |
-Macromolecule #2: Virion associated protein
Macromolecule | Name: Virion associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Ralstonia phage GP4 (virus) |
Molecular weight | Theoretical: 15.819934 KDa |
Sequence | String: MALIQSDFAQ GIRMTPVPDC AGDVTACRFD ITLKNAPAAG DIIELGVLPG NAVPVEAILD VDDLDTGGAP TITLDVGIMS GPVGKNDPA RTCGNELFAA STVGQAGGVV RATASSAFRI QKAEDHRSVG VKVAAGPATG AAGKTIALIL FYVQGTSQ UniProtKB: Virion associated protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40792 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |