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- PDB-8gz7: Octahedral supramolecular assembly of the bicomponent gamma-hemol... -

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Basic information

Entry
Database: PDB / ID: 8gz7
TitleOctahedral supramolecular assembly of the bicomponent gamma-hemolysin octameric pore complexes from Staphylococcus aureus Newman.
Components
  • Gamma-hemolysin component A
  • Gamma-hemolysin component B
KeywordsTOXIN / Super assembly / Pore-forming toxin / cryo-EM / lipid membrane / S. aureus
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / extracellular region
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Gamma-hemolysin component A / Gamma-hemolysin component B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMishra, S. / Roy, A. / Dutta, S.
Funding support India, 2items
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, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-hemolysin component B
C: Gamma-hemolysin component B
E: Gamma-hemolysin component B
G: Gamma-hemolysin component B
B: Gamma-hemolysin component A
D: Gamma-hemolysin component A
F: Gamma-hemolysin component A
H: Gamma-hemolysin component A


Theoretical massNumber of molelcules
Total (without water)247,4778
Polymers247,4778
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area33050 Å2
ΔGint-90 kcal/mol
Surface area85830 Å2

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Components

#1: Protein
Gamma-hemolysin component B / H-gamma-1 / H-gamma-I


Mass: 31305.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hlgB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A077
#2: Protein
Gamma-hemolysin component A / H-gamma-2 / H-gamma-II


Mass: 30563.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hlgA, hlg2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A074

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Octahedral super assembly of bicomponent Gamma-Hemolysin octameric pore complexes
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 3500 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
7Cootmodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11634 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418356
ELECTRON MICROSCOPYf_angle_d0.524828
ELECTRON MICROSCOPYf_dihedral_angle_d4.2132440
ELECTRON MICROSCOPYf_chiral_restr0.0442608
ELECTRON MICROSCOPYf_plane_restr0.0033212

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