+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28226 | |||||||||||||||
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Title | Bacteriophage HRP29 Icosohedral Reconstruction | |||||||||||||||
Map data | ||||||||||||||||
Sample | Shigella phage HRP29 != Shigella phage Buco Shigella phage HRP29
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Keywords | HRP29 / VIRUS | |||||||||||||||
Function / homology | Uncharacterized protein / Putative capsid protein / Uncharacterized protein Function and homology information | |||||||||||||||
Biological species | Shigella phage Buco (virus) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Subramanian S / Bergland Drarvik SM / Parent KN | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: Structure of Shigella bacteriophage HRP29 Authors: Subramanian S / Bergland Drarvik SM / Parent KN | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28226.map.gz | 213.3 MB | EMDB map data format | |
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Header (meta data) | emd-28226-v30.xml emd-28226.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28226_fsc.xml | 27.9 KB | Display | FSC data file |
Images | emd_28226.png | 273.3 KB | ||
Masks | emd_28226_msk_1.map | 1.9 GB | Mask map | |
Others | emd_28226_half_map_1.map.gz emd_28226_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28226 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28226 | HTTPS FTP |
-Validation report
Summary document | emd_28226_validation.pdf.gz | 631.1 KB | Display | EMDB validaton report |
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Full document | emd_28226_full_validation.pdf.gz | 630.7 KB | Display | |
Data in XML | emd_28226_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | emd_28226_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28226 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28226 | HTTPS FTP |
-Related structure data
Related structure data | 8eldMC 8em6C 8es4C C: citing same article (ref.) M: atomic model generated by this map |
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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_28226.map.gz / Format: CCP4 / Size: 1.9 GB / 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: 1.632 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28226_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28226_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28226_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Shigella phage HRP29
Entire | Name: Shigella phage HRP29 |
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Components |
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-Supramolecule #1: Shigella phage Buco
Supramolecule | Name: Shigella phage Buco / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2530183 / Sci species name: Shigella phage Buco / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Shigella flexneri Y (bacteria) |
-Macromolecule #1: Gp37
Macromolecule | Name: Gp37 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella phage Buco (virus) |
Molecular weight | Theoretical: 36.911305 KDa |
Sequence | String: MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT ...String: MANTDYAGNL TRPHWGGAAS DVDIHLEVYQ NEVDTRFQYQ AMFLGLSSQR SVADRSNTYR IDRLNTSSVK GRTSGVALEP TPVRNDKML IVVDTVLYIR NPIDYQDDWT APDFLTEMGQ NNGSEFAEVF DQAHLIQLIK GRSWVAPAHL KPAFSDGIEI E ATIDSDVT TQAGMEANAI AINQAHKAGI DELIKRKVPL NDMITLVSTE IYSLLLEHPK LFNKDWGDAN ANGYKERRAV LM NGIPVVE CTEFPDAGTH PLGSAYTVTA DDAKCRMVTF SKSRTLVTVE AKPFTSRIWD DEQNFANVLD CYAMYQVGER RPD TAAVVK FNEAP UniProtKB: Putative capsid protein |
-Macromolecule #2: Gp47
Macromolecule | Name: Gp47 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella phage Buco (virus) |
Molecular weight | Theoretical: 13.021738 KDa |
Sequence | String: MASIIAAKAK DKQYEIVGKA QNLLKQVQPL YNVGFSTTAL DLLNAYFTYM QAQGFATTRA GTGFVSDGAK LARLDNMLDQ VSKTGYVVL TGTGAPIGET SGTAFDTSFT ALRAAFLAAT TPTTA UniProtKB: Uncharacterized protein |
-Macromolecule #3: Gp48
Macromolecule | Name: Gp48 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Shigella phage Buco (virus) |
Molecular weight | Theoretical: 6.424381 KDa |
Sequence | String: MAVAKATAAQ RQEFLRQLNI LAKDMYQALT QPQDLAYRGP EIDAKIAALE AATAAVKAAS UniProtKB: Uncharacterized 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 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 33.0 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: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |