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- EMDB-36689: alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36689
Titlealpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer
Map dataB-factor sharpened map with B-factor value of -60.
Sample
  • Complex: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag
    • Protein or peptide: alpha hemolysin fused with spy-catcher
    • Protein or peptide: alpha hemolysin fused with spy-tag
Keywordspore / chimera protein / spy-catcher / spy-tag / dimer / TOXIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsIshii Y / Naito K / Yokoyama T / Tanaka Y / Matsuura T
Funding support Japan, 1 items
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, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36689.png

Downloads & links

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Map

FileDownload / File: emd_36689.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map with B-factor value of -60.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å		0.79 Å/pix.
x 400 pix.
= 315.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7916587 - 1.70467
Average (Standard dev.)0.0021757274 (±0.05315071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 315.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: One of the half maps.

Fileemd_36689_half_map_1.map
AnnotationOne of the half maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps.

Fileemd_36689_half_map_2.map
AnnotationOne of the half maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher ...

EntireName: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag
Components
  • Complex: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag
    • Protein or peptide: alpha hemolysin fused with spy-catcher
    • Protein or peptide: alpha hemolysin fused with spy-tag

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Supramolecule #1: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher ...

SupramoleculeName: heptameric alpha hemolysin (K237C) pore dimerized by spy-catcher and spy-tag
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: alpha hemolysin fused with spy-catcher

MacromoleculeName: alpha hemolysin fused with spy-catcher / type: protein_or_peptide / ID: 1 / Details: 300-412:SpyCatcher / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 46.977469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String:
MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRC AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSVTTLSGLS GEQGPSGDMT TEE DSATHI KFSKRDEDGR ELAGATMELR DSSGKTISTW ISDGHVKDFY LYPGKYTFVE TAAPDGYEVA TPIEFTVNED GQVT VDGEA TEGDAHTGGS HHHHHH

UniProtKB: Alpha-hemolysin

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Macromolecule #2: alpha hemolysin fused with spy-tag

MacromoleculeName: alpha hemolysin fused with spy-tag / type: protein_or_peptide / ID: 2 / Details: 300-315:SpyTag / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 36.777898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW ...String:
MADSDINIKT GTTDIGSNTT VKTGDLVTYD KENGMHKKVF YSFIDDKNHN KKLLVIRTKG TIAGQYRVYS EEGANKSGLA WPSAFKVQL QLPDNEVAQI SDYYPRNSID TKEYMSTLTY GFNSNVTGDD TGKIGGLIGA NVSIGHTLRY VQPDFKTILE S PTDKKVGW KVIFNNMVNQ NWGPYDRDSW NPVYGNQLFM KTRNGSMKAA DNFLDPNKAS SLLSSGFSPD FATVITMDRC AS KQQTNID VIYERVRDDY QLHWTSTNWK GTNTKDKWTD RSSERYKIDW EKEEMTNGSS GSRGVPHIVM VDAYKRYKGG SHH HHHH

UniProtKB: Alpha-hemolysin

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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

Concentration0.58 mg/mL
BufferpH: 7.6
Component:
ConcentrationName
20.0 mMHEPES-KOH
50.0 mMPotassium glutamate

Details: 20mM HEPES-KOH[pH7.6], 50mM Potassium glutamate
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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