+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44518 | |||||||||
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Title | Pseudomonas phage DEV 5-fold vertex (major coat protein) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virion coat / complex / STRUCTURAL PROTEIN / gp77 | |||||||||
Function / homology | Major coat protein Function and homology information | |||||||||
Biological species | Pseudomonas phage vB_PaeP_DEV (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Iglesias SM / Hou CFD / Li F / Cingolani G | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Integrative structural analysis of Pseudomonas phage DEV reveals a genome ejection motor Authors: Lokareddy R / Hou CFD / Forti F / Iglesias SM / Li F / Pavlenok M / Niederweis M / Briani F / Cingolani G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44518.map.gz | 472.9 MB | EMDB map data format | |
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Header (meta data) | emd-44518-v30.xml emd-44518.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44518_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_44518.png | 104.1 KB | ||
Masks | emd_44518_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-44518.cif.gz | 5.4 KB | ||
Others | emd_44518_half_map_1.map.gz emd_44518_half_map_2.map.gz | 412.9 MB 411.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44518 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44518 | HTTPS FTP |
-Validation report
Summary document | emd_44518_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_44518_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_44518_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | emd_44518_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44518 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44518 | HTTPS FTP |
-Related structure data
Related structure data | 9bgnMC 9bgmC 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_44518.map.gz / Format: CCP4 / Size: 512 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
-Mask #1
File | emd_44518_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44518_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44518_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Major coat protein of Pseudomonas phage DEV
Entire | Name: Major coat protein of Pseudomonas phage DEV |
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Components |
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-Supramolecule #1: Major coat protein of Pseudomonas phage DEV
Supramolecule | Name: Major coat protein of Pseudomonas phage DEV / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas phage vB_PaeP_DEV (virus) |
-Macromolecule #1: gp77 major coat protein
Macromolecule | Name: gp77 major coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeP_DEV (virus) |
Molecular weight | Theoretical: 44.114113 KDa |
Recombinant expression | Organism: Pseudomonas (RNA similarity group I) |
Sequence | String: MAGPVDNIKP MKYNDPANGV ESSIGPQIHT RYWYKRALID AAKEAYFGQL ADTFSMPKHY GKEIVRLHYI PLLDDRNVND QGIDASGAT IANGNLYGSS RDVGNITAKM PTLTEIGGRV NRVGFKRVEI KGKLEKYGFF REYTQEQLDF DSDPAMEGHV T TEMVKGAN ...String: MAGPVDNIKP MKYNDPANGV ESSIGPQIHT RYWYKRALID AAKEAYFGQL ADTFSMPKHY GKEIVRLHYI PLLDDRNVND QGIDASGAT IANGNLYGSS RDVGNITAKM PTLTEIGGRV NRVGFKRVEI KGKLEKYGFF REYTQEQLDF DSDPAMEGHV T TEMVKGAN EITEDLLQID LLNSAGTVRY PGAATSDAEV DASTEVTYDS LMRLRLDLDN ARAPTKIKMI TGTRMIDTRT VG NARALYV GSDLVPTIEA MKDNHGNPAF IPIEKYAAGG ATMHGEVGQL GRFRVIVNPQ MMHWAGVGKA VDPNDQVPMH ESG GKYSVF PMLCVASEAF TTVGFATDGK NVKFKIITKR PGEATADRSD PYGEMGFMSI KWYYGFMVFR PEWIALLKTV ARL UniProtKB: Major coat 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 TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |