+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26159 | |||||||||
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Title | Cryo-EM of AFV6 | |||||||||
Map data | Cryo-EM of AFV6 | |||||||||
Sample |
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Keywords | helical symmetry / archaeal virus / VIRUS | |||||||||
Function / homology | Structural protein / Structural protein Function and homology information | |||||||||
Biological species | Acidianus filamentous virus 6 | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Wang F / Cvirkaite-Krupovic V | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM of AFV6 Authors: Wang F / Cvirkaite-Krupovic V / Krupovic M / Egelman EH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26159.map.gz | 18.7 MB | EMDB map data format | |
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Header (meta data) | emd-26159-v30.xml emd-26159.xml | 10.5 KB 10.5 KB | Display Display | EMDB header |
Images | emd_26159.png | 134 KB | ||
Filedesc metadata | emd-26159.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26159 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26159 | HTTPS FTP |
-Validation report
Summary document | emd_26159_validation.pdf.gz | 471.1 KB | Display | EMDB validaton report |
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Full document | emd_26159_full_validation.pdf.gz | 470.7 KB | Display | |
Data in XML | emd_26159_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_26159_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26159 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26159 | HTTPS FTP |
-Related structure data
Related structure data | 7txjMC 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 |
EM raw data | EMPIAR-11040 (Title: Micrographs of viruses ATV and AFV6 / Data size: 218.0 Data #1: raw micrographs and gain reference [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26159.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM of AFV6 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Acidianus filamentous virus 6
Entire | Name: Acidianus filamentous virus 6 |
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Components |
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-Supramolecule #1: Acidianus filamentous virus 6
Supramolecule | Name: Acidianus filamentous virus 6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 346882 / Sci species name: Acidianus filamentous virus 6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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-Macromolecule #1: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3')
Macromolecule | Name: DNA (5'-D(*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*A)-3') / type: dna / ID: 1 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Acidianus filamentous virus 6 |
Molecular weight | Theoretical: 3.65944 KDa |
Sequence | String: (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA) |
-Macromolecule #2: MCP1
Macromolecule | Name: MCP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Acidianus filamentous virus 6 |
Molecular weight | Theoretical: 18.593428 KDa |
Sequence | String: MAGKKRRLSQ ASVLRYYAKR FTMNVGTTAH VLGKEVAGNP WVAKAIDKLS YQETYNWISD YQASHLAKQV AKQVAEKYGI PPTFQGLLM AYAEKVVANY ILDYKGESLT QMHDNYLYEL MQKMPIAPTG TSSGYIYVFI GKDGKTHTVD MSKVLTDIED A LLKRA UniProtKB: Structural protein |
-Macromolecule #3: MCP2
Macromolecule | Name: MCP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Acidianus filamentous virus 6 |
Molecular weight | Theoretical: 22.751678 KDa |
Sequence | String: MAGRQAHRKF DVRNDTSTRW KGKLYGIFVN YMGEDYAKEF VEQAYSNYEK VFVNIYTKIH NQLRTTLTSS AGAGATFPLW QIINEAIYA VYLTHKETAS FLYAKYVARG IQPNVVKKIL AETGNALKGI VPAVAQELGE TVLDESNVIS VVDDIVRKNP A LPNSYAGI ...String: MAGRQAHRKF DVRNDTSTRW KGKLYGIFVN YMGEDYAKEF VEQAYSNYEK VFVNIYTKIH NQLRTTLTSS AGAGATFPLW QIINEAIYA VYLTHKETAS FLYAKYVARG IQPNVVKKIL AETGNALKGI VPAVAQELGE TVLDESNVIS VVDDIVRKNP A LPNSYAGI ILQEARISTT PHYEGTEGFS SMESAYSALE EIEKGL UniProtKB: Structural protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6 |
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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: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 5.75 Å Applied symmetry - Helical parameters - Δ&Phi: 38.46 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78141 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |