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- EMDB-34391: Octahedral supramolecular assembly of the bicomponent gamma-hemol... -
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Open data
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Basic information
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Title | Octahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman. | |||||||||
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![]() | Super assembly / Pore-forming toxin / cryo-EM / lipid membrane / S. aureus / TOXIN | |||||||||
Function / homology | Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / cytolysis in another organism / toxin activity / extracellular region / Gamma-hemolysin component A / Gamma-hemolysin component B![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Mishra S / Roy A / Dutta S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Octahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman. Authors: Mishra S / Roy A / Dutta S | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 60.9 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 225.6 MB 225.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gz7MC 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
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Voxel size | X=Y=Z: 0.92 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34391_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34391_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Octahedral super assembly of bicomponent Gamma-Hemolysin octameri...
Entire | Name: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes |
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Components |
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-Supramolecule #1: Octahedral super assembly of bicomponent Gamma-Hemolysin octameri...
Supramolecule | Name: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Gamma-hemolysin component B
Macromolecule | Name: Gamma-hemolysin component B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 31.305635 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KVTLYKTTAT ADSDKFKISQ ILTFNFIKDK SYDKDTLVLK ATGNINSGFV KPNPNDYDFS KLYWGAKYNV SISSQSNDSV NVVDYAPKN QNEEFQVQNT LGYTFGGNTA FSETINYKQE SYRTTLSRNT NYKNVGWGVE AHKIMNNGWG PYGRDSFHPT Y GNELFLAG ...String: KVTLYKTTAT ADSDKFKISQ ILTFNFIKDK SYDKDTLVLK ATGNINSGFV KPNPNDYDFS KLYWGAKYNV SISSQSNDSV NVVDYAPKN QNEEFQVQNT LGYTFGGNTA FSETINYKQE SYRTTLSRNT NYKNVGWGVE AHKIMNNGWG PYGRDSFHPT Y GNELFLAG RQSSAYAGQN FIAQHQMPLL SRSNFNPEFL SVLSHRQDGA KKSKITVTYQ REMDLYQIRW NGFYWAGANY KN FKTRTFK STYEIDWENH KVKLLDTKET ENNK UniProtKB: Gamma-hemolysin component B |
-Macromolecule #2: Gamma-hemolysin component A
Macromolecule | Name: Gamma-hemolysin component A / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.563545 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KIEDIGQGAE IIKRTQDITS KRLAITQNIQ FDFVKDKKYN KDALVVKMQG FISSRTTYSD LKKYPYIKRM IWPFQYNISL KTKDSNVDL INYLPKNKID SADVSQKLGY NIGSFNYSKT ISYNQKNYVT EVESQNSKGV KWGVKANSFV TPNGQVSAYD Q YLFAQDPT ...String: KIEDIGQGAE IIKRTQDITS KRLAITQNIQ FDFVKDKKYN KDALVVKMQG FISSRTTYSD LKKYPYIKRM IWPFQYNISL KTKDSNVDL INYLPKNKID SADVSQKLGY NIGSFNYSKT ISYNQKNYVT EVESQNSKGV KWGVKANSFV TPNGQVSAYD Q YLFAQDPT GPAARDYFVP DNQLPPLIQS GFNPSFITTL SHERGKGDKS EFEITYGRNM DATYAYVTRH RLAVDRKHDA FK NRNVTVK YEVNWKTHEV KIKSITPK UniProtKB: Gamma-hemolysin component A |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 3.5 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-8gz7: |