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- EMDB-34391: Octahedral supramolecular assembly of the bicomponent gamma-hemol... -

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Basic information

Entry
Database: EMDB / ID: EMD-34391
TitleOctahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman.
Map data
Sample
  • Complex: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes
    • Protein or peptide: Gamma-hemolysin component B
    • Protein or peptide: Gamma-hemolysin component A
KeywordsSuper assembly / Pore-forming toxin / cryo-EM / lipid membrane / S. aureus / TOXIN
Function / homologyBi-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 speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMishra S / Roy A / Dutta S
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22844/2017 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
CitationJournal: 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
DepositionSep 26, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_34391.png

Downloads & links

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Map

FileDownload / File: emd_34391.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.427
Minimum - Maximum-1.5703856 - 2.6762927
Average (Standard dev.)0.016665597 (±0.13193119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34391_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34391_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octahedral super assembly of bicomponent Gamma-Hemolysin octameri...

EntireName: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes
Components
  • Complex: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes
    • Protein or peptide: Gamma-hemolysin component B
    • Protein or peptide: Gamma-hemolysin component A

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Supramolecule #1: Octahedral super assembly of bicomponent Gamma-Hemolysin octameri...

SupramoleculeName: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Gamma-hemolysin component B

MacromoleculeName: Gamma-hemolysin component B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 31.305635 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: Gamma-hemolysin component A

MacromoleculeName: Gamma-hemolysin component A / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 30.563545 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11634
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8gz7:
Octahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman.

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