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Yorodumi- EMDB-34391: Octahedral supramolecular assembly of the bicomponent gamma-hemol... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34391 | |||||||||
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Title | Octahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman. | |||||||||
Map data | ||||||||||
Sample |
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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 Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Mishra S / Roy A / Dutta S | |||||||||
Funding support | India, 2 items
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Citation | Journal: To Be Published 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 | emd_34391.map.gz | 229.6 MB | EMDB map data format | |
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Header (meta data) | emd-34391-v30.xml emd-34391.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34391_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_34391.png | 60.9 KB | ||
Others | emd_34391_half_map_1.map.gz emd_34391_half_map_2.map.gz | 225.6 MB 225.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34391 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34391 | HTTPS FTP |
-Related structure data
Related structure data | 8gz7MC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34391.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-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 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Staphylococcus aureus (bacteria) |
-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: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 31.305635 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
-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: Staphylococcus aureus (bacteria) |
Molecular weight | Theoretical: 30.563545 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 3.5 µm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-8gz7: |