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- EMDB-36689: alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer | |||||||||
![]() | B-factor sharpened map with B-factor value of -60. | |||||||||
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![]() | pore / chimera protein / spy-catcher / spy-tag / dimer / TOXIN | |||||||||
Function / homology | ![]() cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
![]() | Ishii Y / Naito K / Yokoyama T / Tanaka Y / Matsuura T | |||||||||
Funding support | ![]()
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![]() | ![]() Title: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer Authors: Ishii Y / Naito K / Yokoyama T / Tanaka Y / Matsuura T | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 126.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.1 KB 16.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 82.6 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() | 226.6 MB 226.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 898.4 KB | Display | ![]() |
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Full document | ![]() | 898 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jx3MC ![]() 8jx2C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | B-factor sharpened map with B-factor value of -60. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.788 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: One of the half maps.
File | emd_36689_half_map_1.map | ||||||||||||
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Annotation | One of the half maps. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: One of the half maps.
File | emd_36689_half_map_2.map | ||||||||||||
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Annotation | One of the half maps. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher ...
Entire | Name: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag |
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Components |
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-Supramolecule #1: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher ...
Supramolecule | Name: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: alpha hemolysin fused with spy-catcher
Macromolecule | Name: alpha hemolysin fused with spy-catcher / type: protein_or_peptide / ID: 1 / Details: 300-412:SpyCatcher / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.977469 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRC AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSVTTLSGLS GEQGPSGDMT TEE DSATHI KFSKRDEDGR ELAGATMELR DSSGKTISTW ISDGHVKDFY LYPGKYTFVE TAAPDGYEVA TPIEFTVNED GQVT VDGEA TEGDAHTGGS HHHHHH UniProtKB: Alpha-hemolysin |
-Macromolecule #2: alpha hemolysin fused with spy-tag
Macromolecule | Name: alpha hemolysin fused with spy-tag / type: protein_or_peptide / ID: 2 / Details: 300-315:SpyTag / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.777898 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRC AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSRGVPHIVM VDAYKRYKGG SHH HHHH UniProtKB: Alpha-hemolysin |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.58 mg/mL | ||||||
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Buffer | pH: 7.6 Component:
Details: 20mM HEPES-KOH[pH7.6], 50mM Potassium glutamate | ||||||
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm |