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- EMDB-23066: Protective antigen pore translocating lethal factor N-terminal domain -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23066 | |||||||||
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Title | Protective antigen pore translocating lethal factor N-terminal domain | |||||||||
![]() | Anthrax Toxin Translocation Complex | |||||||||
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![]() | translocation / ![]() ![]() ![]() | |||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Machen AJ / Freudenthal BD | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
Images | ![]() | 43.3 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kxrMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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: ![]() ![]() ![]() |
-Macromolecule #1: Lethal factor
Macromolecule | Name: Lethal factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 30.520408 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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: ![]() ![]() ![]() |
Molecular weight | Theoretical: 63.019012 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
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 | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 5.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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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) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122651 |