+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36150 | |||||||||
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Title | Cryo-EM structure of Vibrio campbellii alpha-hemolysin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Vibrio campbellii alpha-hemolysin / Pore-forming toxins (PFTs) / Calcium-dependent oligomerization / Membrane association / Structure-function relationship / TOXIN | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Vibrio campbellii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.06 Å | |||||||||
Authors | Wang CH / Yeh MK / Ho MC / Lin SM | |||||||||
Funding support | Taiwan, 2 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for calcium-stimulating pore formation of Vibrio α-hemolysin. Authors: Yu-Chuan Chiu / Min-Chi Yeh / Chun-Hsiung Wang / Yu-An Chen / Hsiang Chang / Han-You Lin / Meng-Chiao Ho / Shih-Ming Lin / Abstract: Vibrio α-hemolysins (αHLs) are β-pore-forming toxins secreted by Vibrio pathogens, crucial for the facilitation of bacterial infections through host cell lysis. These toxins are produced as ...Vibrio α-hemolysins (αHLs) are β-pore-forming toxins secreted by Vibrio pathogens, crucial for the facilitation of bacterial infections through host cell lysis. These toxins are produced as inactive precursors, requiring proteolytic maturation and membrane association for activation within host tissues. Here, we investigate Vibrio campbellii αHL (VcαHL), and establish that its hemolytic activity is significantly stimulated by calcium ions, with an EC that aligns with physiological calcium concentrations. Furthermore, we illustrate the vital contribution of calcium ions to the oligomerization of VcαHL on membranes. Using X-ray crystallography and cryo-electron microscopy, we decipher both the immature and assembled structures of VcαHL and elucidate the conformational changes corresponding to toxin assembly. We also identify a calcium-binding module that is integral for VcαHL's calcium-dependent activation. These findings provide insights into the regulatory mechanisms of VcαHL and have the potential to inform the development of targeted therapeutic strategies against Vibrio infections. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36150.map.gz | 944.3 MB | EMDB map data format | |
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Header (meta data) | emd-36150-v30.xml emd-36150.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36150_fsc.xml | 23 KB | Display | FSC data file |
Images | emd_36150.png | 200.4 KB | ||
Filedesc metadata | emd-36150.cif.gz | 5.9 KB | ||
Others | emd_36150_additional_1.map.gz emd_36150_half_map_1.map.gz emd_36150_half_map_2.map.gz | 499 MB 928.9 MB 928.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36150 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36150 | HTTPS FTP |
-Related structure data
Related structure data | 8jc7MC 8jbqC 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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-Map
File | Download / File: emd_36150.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.5305 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpen map
File | emd_36150_additional_1.map | ||||||||||||
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Annotation | unsharpen map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36150_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36150_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : heptameric ring-shaped complex of Vibrio campbellii alpha-hemolysin
Entire | Name: heptameric ring-shaped complex of Vibrio campbellii alpha-hemolysin |
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Components |
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-Supramolecule #1: heptameric ring-shaped complex of Vibrio campbellii alpha-hemolysin
Supramolecule | Name: heptameric ring-shaped complex of Vibrio campbellii alpha-hemolysin type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Vibrio campbellii (bacteria) |
-Macromolecule #1: Hemolysin
Macromolecule | Name: Hemolysin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio campbellii (bacteria) |
Molecular weight | Theoretical: 80.643578 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNINEPSGEA ANIISQAADS HAMKYYNAAD WQAEDNALPS LAELRDLVIN QQKSVLFDFS QNSDADGQAE MQAQFRKTYG VGFANQFIF ITEHKGELLF TPFEHSEEVD PKLLEAPLTT RSGLKSTAPT NSETSTLPHV AFYISVNRPI SDEECTFDNS W LWKDEKGS ...String: MNINEPSGEA ANIISQAADS HAMKYYNAAD WQAEDNALPS LAELRDLVIN QQKSVLFDFS QNSDADGQAE MQAQFRKTYG VGFANQFIF ITEHKGELLF TPFEHSEEVD PKLLEAPLTT RSGLKSTAPT NSETSTLPHV AFYISVNRPI SDEECTFDNS W LWKDEKGS RPFCKDANIS LIYRVNLERS LQYGIVGSAT PNAKIVRISL DDDSSGAGIH LNDQLSYRRF GASYTTLDAY FR EWSTDAI AQDYRFVFKT SNNKAEILET FPIDNLNVKY EKRKQSGFEL GVTGGAEVSE DGPKAKLEAR ASITQSRWLT YNT QDYRVE RNAKNAQTVS FTWNRQEYAT AESLLNRSTD ALWVDTYPVD VNRISPLSYA SFVPKMDVIY KASDTETGST DFII DSSVN IRPIYNGAYK HYYVVGAHQS YHGFENSPRR RITKSASFTV DWDHPVFTGG RPVNLQLASF NNRCVQVDAQ SRLTA NTCD DQQSAQSFIY DQLGRYVSAS NTELCLDGAA LDVLQTCNQN LTQRWEWRKN TDELTNVYSG ESLGHDKQTG ELGLYA SSN DAVSLRTITA YTNVFNVQKS SPILGYTQGK MNQQSVGQNY RLYVREGSAI DALGTASDLL VGGNGGSLTS VDLSGVK SI TATSGDFQYG GQQLVALTFT YQDGRQQMVG SKAHVTNAHE DRFDLPDAAK ITQLNIWADD WLVKGVQFDL NLEHHHHH H UniProtKB: UNIPROTKB: A0A344KRS4 |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 591 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |