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Yorodumi- EMDB-23066: Protective antigen pore translocating lethal factor N-terminal domain -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23066 | |||||||||
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Title | Protective antigen pore translocating lethal factor N-terminal domain | |||||||||
Map data | Anthrax Toxin Translocation Complex | |||||||||
Sample |
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Keywords | translocation / complex / anthrax / refolding / TOXIN | |||||||||
Function / homology | Function and homology information anthrax lethal factor endopeptidase / positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / metalloendopeptidase activity / metallopeptidase activity / toxin activity ...anthrax lethal factor endopeptidase / positive regulation of apoptotic process in another organism / host cell cytosol / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / host cell endosome membrane / protein homooligomerization / metalloendopeptidase activity / metallopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / identical protein binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Bacillus anthracis (anthrax bacterium) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Machen AJ / Freudenthal BD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Rep / Year: 2021 Title: Anthrax toxin translocation complex reveals insight into the lethal factor unfolding and refolding mechanism. Authors: Alexandra J Machen / Mark T Fisher / Bret D Freudenthal / Abstract: Translocation is essential to the anthrax toxin mechanism. Protective antigen (PA), the binding component of this AB toxin, forms an oligomeric pore that translocates lethal factor (LF) or edema ...Translocation is essential to the anthrax toxin mechanism. Protective antigen (PA), the binding component of this AB toxin, forms an oligomeric pore that translocates lethal factor (LF) or edema factor, the active components of the toxin, into the cell. Structural details of the translocation process have remained elusive despite their biological importance. To overcome the technical challenges of studying translocation intermediates, we developed a method to immobilize, transition, and stabilize anthrax toxin to mimic important physiological steps in the intoxication process. Here, we report a cryoEM snapshot of PA translocating the N-terminal domain of LF (LF). The resulting 3.3 Å structure of the complex shows density of partially unfolded LF near the canonical PA binding site. Interestingly, we also observe density consistent with an α helix emerging from the 100 Å β barrel channel suggesting LF secondary structural elements begin to refold in the pore channel. We conclude the anthrax toxin β barrel aids in efficient folding of its enzymatic payload prior to channel exit. Our hypothesized refolding mechanism has broader implications for pore length of other protein translocating toxins. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23066.map.gz | 2.6 MB | EMDB map data format | |
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Header (meta data) | emd-23066-v30.xml emd-23066.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_23066.png | 43.3 KB | ||
Filedesc metadata | emd-23066.cif.gz | 5.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23066 | HTTPS FTP |
-Validation report
Summary document | emd_23066_validation.pdf.gz | 391.7 KB | Display | EMDB validaton report |
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Full document | emd_23066_full_validation.pdf.gz | 391.2 KB | Display | |
Data in XML | emd_23066_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_23066_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23066 | HTTPS FTP |
-Related structure data
Related structure data | 7kxrMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23066.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Anthrax Toxin Translocation Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.605 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Anthrax toxin protective antigen translocating lethal factor N-te...
Entire | Name: Anthrax toxin protective antigen translocating lethal factor N-terminal domain |
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Components |
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-Supramolecule #1: Anthrax toxin protective antigen translocating lethal factor N-te...
Supramolecule | Name: Anthrax toxin protective antigen translocating lethal factor N-terminal domain type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
-Macromolecule #1: Lethal factor
Macromolecule | Name: Lethal factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: anthrax lethal factor endopeptidase |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 30.520408 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYCPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ ...String: AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYCPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ KFLDVLNTIK NASDSDGQDL LFTNQLKEHP TDFSVEFLEQ NSNEVQEVFA KAFAYYIEPQ HRDVLQLYAP EA FNYMDKF NEQEINLSLE ELKDQR UniProtKB: Lethal factor |
-Macromolecule #2: Protective antigen
Macromolecule | Name: Protective antigen / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 63.019012 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TVPDRDNDGI PDSLEVEGYT VDVKNKRTFL SPWISNIHEK KGLTKYKSSP EKWSTASDPY SDFEKVTGRI DKNVSPEARH PLVAAYPIV HVDMENIILS KNEDQSTQNT DSQTRTISKN TSTSRTHTSE VHGNAEVHAS FFDIGGSVSA GFSNSNSSTV A IDHSLSLA ...String: TVPDRDNDGI PDSLEVEGYT VDVKNKRTFL SPWISNIHEK KGLTKYKSSP EKWSTASDPY SDFEKVTGRI DKNVSPEARH PLVAAYPIV HVDMENIILS KNEDQSTQNT DSQTRTISKN TSTSRTHTSE VHGNAEVHAS FFDIGGSVSA GFSNSNSSTV A IDHSLSLA GERTWAETMG LNTADTARLN ANIRYVNTGT APIYNVLPTT SLVLGKNQTL ATIKAKENQL SQILAPNNYY PS KNLAPIA LNAQDDFSST PITMNYNQFL ELEKTKQLRL DTDQVYGNIA TYNFENGRVR VDTGSNWSEV LPQIQETTAR IIF NGKDLN LVERRIAAVN PSDPLETTKP DMTLKEALKI AFGFNEPNGN LQYQGKDITE FDFNFDQQTS QNIKNQLAEL NATN IYTVL DKIKLNAKMN ILIRDKRFHY DRNNIAVGAD ESVVKEAHRE VINSSTEGLL LNIDKDIRKI LSGYIVEIED TEGLK EVIN DRYDMLNISS LRQDGKTFID FKKYNDKLPL YISNPNYKVN VYAVTKENTI INPSENGDTS TNGIKKILIF SKKGYE IG UniProtKB: Protective antigen |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122651 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15) / Details: ab initio |
Final angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 3.0.1) |