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Yorodumi- EMDB-28604: Acheta domesticus segmented densovirus high buoyancy fraction 2 e... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28604 | ||||||||||||
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Title | Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure | ||||||||||||
Map data | Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure | ||||||||||||
Sample |
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Keywords | parvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Capsid protein Function and homology information | ||||||||||||
Biological species | Solenopsis invicta-associated densovirus / unclassified Densovirinae (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Penzes JJ / McKenna R / Tijssen P | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: To Be Published Title: Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome Authors: Penzes JJ / Pham HT / Chipman P / Smith E / McKenna R / Tijssen P | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28604.map.gz | 442.6 MB | EMDB map data format | |
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Header (meta data) | emd-28604-v30.xml emd-28604.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | emd_28604.png | 240.9 KB | ||
Filedesc metadata | emd-28604.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28604 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28604 | HTTPS FTP |
-Validation report
Summary document | emd_28604_validation.pdf.gz | 519.6 KB | Display | EMDB validaton report |
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Full document | emd_28604_full_validation.pdf.gz | 519.1 KB | Display | |
Data in XML | emd_28604_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | emd_28604_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28604 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28604 | HTTPS FTP |
-Related structure data
Related structure data | 8eu5MC 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_28604.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Acheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : unclassified Densovirinae
Entire | Name: unclassified Densovirinae (virus) |
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Components |
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-Supramolecule #1: unclassified Densovirinae
Supramolecule | Name: unclassified Densovirinae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 185880 / Sci species name: unclassified Densovirinae / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Virus shell | Shell ID: 1 / Diameter: 210.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Solenopsis invicta-associated densovirus |
Molecular weight | Theoretical: 36.291906 KDa |
Recombinant expression | Organism: Acheta domesticus (house cricket) |
Sequence | String: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP ...String: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP TREKWCHTWD LDVLNHNYLW EPNNLDSQWT LIPGAQAVQP TATPIGPTYQ EIVIATKAIG ANESALVTTI QD RRSYPRL MLSQPQIKDE TDTMKFKYQI RISTELEMEH HIKPDIANPW LTRQTLPLPA LSGDGTTRYV PCVPYETHVS Q UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Name: Phosphate-buffered saline |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
Details | Deceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 4.32 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |