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- PDB-8jx2: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer -

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Basic information

Entry
Database: PDB / ID: 8jx2
Titlealpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
Components
  • alpha hemolysin fused with spy-catcher
  • alpha hemolysin fused with spy-tag
KeywordsTOXIN / pore / chimera protein / spy-catcher / spy-tag / dimer
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsIshii, Y. / Naito, K. / Yokoyama, T. / Tanaka, Y. / Matsuura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
Authors: Ishii, Y. / Naito, K. / Yokoyama, T. / Tanaka, Y. / Matsuura, T.
History
DepositionJun 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 3, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha hemolysin fused with spy-catcher
B: alpha hemolysin fused with spy-catcher
C: alpha hemolysin fused with spy-catcher
D: alpha hemolysin fused with spy-catcher
E: alpha hemolysin fused with spy-catcher
F: alpha hemolysin fused with spy-catcher
G: alpha hemolysin fused with spy-catcher
H: alpha hemolysin fused with spy-tag
I: alpha hemolysin fused with spy-tag
J: alpha hemolysin fused with spy-tag
K: alpha hemolysin fused with spy-tag
L: alpha hemolysin fused with spy-tag
M: alpha hemolysin fused with spy-tag
N: alpha hemolysin fused with spy-tag


Theoretical massNumber of molelcules
Total (without water)586,65214
Polymers586,65214
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
alpha hemolysin fused with spy-catcher / Alpha-HL / Alpha-toxin


Mass: 47003.504 Da / Num. of mol.: 7 / Mutation: G122S,K147R
Source method: isolated from a genetically manipulated source
Details: 300-412:SpyCatcher / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
#2: Protein
alpha hemolysin fused with spy-tag / Alpha-HL / Alpha-toxin


Mass: 36803.934 Da / Num. of mol.: 7 / Mutation: G122S,K147R
Source method: isolated from a genetically manipulated source
Details: 300-315:SpyTag / Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
Has protein modificationN

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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: heptameric alpha hemolysin pore dimerized by spy-catcher and spy-tag
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6 / Details: 20mM HEPES-KOH[pH7.6], 50mM Potassium glutamate
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES-KOH1
250 mMPotassium glutamate1
SpecimenConc.: 0.58 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
11cryoSPARC4.2.1final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349752 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00233600
ELECTRON MICROSCOPYf_angle_d0.47745486
ELECTRON MICROSCOPYf_dihedral_angle_d4.0844438
ELECTRON MICROSCOPYf_chiral_restr0.0444872
ELECTRON MICROSCOPYf_plane_restr0.0035866

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