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Yorodumi- EMDB-44519: Pseudomonas phage DEV gp72 ejection protein (pre-ejection conform... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44519 | |||||||||
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Title | Pseudomonas phage DEV gp72 ejection protein (pre-ejection conformation) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | virion scaffolding / complex / STRUCTURAL PROTEIN / gp72 / ejection protein | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Pseudomonas phage vB_PaeP_DEV (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 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_44519.map.gz | 397.2 MB | EMDB map data format | |
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Header (meta data) | emd-44519-v30.xml emd-44519.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44519_fsc.xml | 18.1 KB | Display | FSC data file |
Images | emd_44519.png | 45.9 KB | ||
Masks | emd_44519_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-44519.cif.gz | 5.4 KB | ||
Others | emd_44519_half_map_1.map.gz emd_44519_half_map_2.map.gz | 402.3 MB 403.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44519 | HTTPS FTP |
-Validation report
Summary document | emd_44519_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_44519_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_44519_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | emd_44519_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44519 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44519 | HTTPS FTP |
-Related structure data
Related structure data | 9bgoMC 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_44519.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_44519_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44519_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_44519_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Scaffolding protein of Pseudomonas phage DEV
Entire | Name: Scaffolding protein of Pseudomonas phage DEV |
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Components |
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-Supramolecule #1: Scaffolding protein of Pseudomonas phage DEV
Supramolecule | Name: Scaffolding 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: gp72
Macromolecule | Name: gp72 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage vB_PaeP_DEV (virus) |
Molecular weight | Theoretical: 57.183238 KDa |
Recombinant expression | Organism: Pseudomonas aeruginosa (bacteria) |
Sequence | String: MAQEITWRNI GATVSPGSAS SMSAGTTGVQ QALGALGDII SRQQEMNVNN AKLQREANTQ SYLDQVAAST LEQLSNADYR SGLEAQRDA MGMNLDRAAT RDAITKQISA QQNQAAATQK FDDMQAEVGQ RGIVDQLRTL SAEGRAGEVN QILAEQQLIN E GEIRKELT ...String: MAQEITWRNI GATVSPGSAS SMSAGTTGVQ QALGALGDII SRQQEMNVNN AKLQREANTQ SYLDQVAAST LEQLSNADYR SGLEAQRDA MGMNLDRAAT RDAITKQISA QQNQAAATQK FDDMQAEVGQ RGIVDQLRTL SAEGRAGEVN QILAEQQLIN E GEIRKELT GVQDAIQNRQ YRAAGEQRAQ AAANRAAEAH SLSMAAGREN LAFTREQRDE LRRDRDEAKL VSGTIATTFQ DY DESRQAQ SEIMRIVGKE VGMPTDDQGM PDMSRASQDQ LDAFSNALNE AGVQANTSPT ERRNAVLKSL VDAGVSSKGI AQA KQEMEL RESLEGLAPQ DRTKVEATIG AVNAELDTLQ RTATEDYERE VARNPFVEPD KDPLGSVNKI VDKAVKSGFG WEGD RQDLN NMLVDFATNG IKLPDGRTAV VPSKLLEQAF NTTNTWLFKN AGDVEKRIIE LMTTDGMTQM REDAPTIREN FLKTV SDIA NQKRSNAVKV TRSAEREKGV TMDPTDDLTF ALRGRKR 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 |
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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 |