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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21694 | ||||||||||||
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Title | Anthrax octamer prechannel bound to full-length lethal factor | ||||||||||||
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![]() | translocase / anthrax toxin / protective antigen / lethal factor / octamer | ||||||||||||
Function / homology | ![]() 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 ...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 | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Zhou K / Hardenbrook NJ | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic Structures of Anthrax Prechannel Bound with Full-Length Lethal and Edema Factors. Authors: Kang Zhou / Shiheng Liu / Nathan J Hardenbrook / Yanxiang Cui / Bryan A Krantz / Z Hong Zhou / ![]() Abstract: Pathogenesis of anthrax disease involves two cytotoxic enzymes-edema factor (EF) and lethal factor (LF)-which are individually recruited by the protective antigen heptamer (PA) or octamer (PA) ...Pathogenesis of anthrax disease involves two cytotoxic enzymes-edema factor (EF) and lethal factor (LF)-which are individually recruited by the protective antigen heptamer (PA) or octamer (PA) prechannel and subsequently translocated across channels formed on the endosomal membrane upon exposure to low pH. Here, we report the atomic structures of PA prechannel-bound full-length EF and LF. In this pretranslocation state, the N-terminal segment of both factors refolds into an α helix engaged in the α clamp of the prechannel. Recruitment to the PA prechannel exposes an originally buried β strand of both toxins and enables domain organization of EF. Many interactions occur on domain interfaces in both PA prechannel-bound EF and LF, leading to toxin compaction prior to translocation. Our results provide key insights into the molecular mechanisms of translocation-coupled protein unfolding and translocation. | ||||||||||||
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 | ![]() | 95.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.3 KB 16.3 KB | Display Display | ![]() |
Images | ![]() | 249 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wjjMC ![]() 6vraC C: citing same article ( M: atomic model generated by this map |
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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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Voxel size | X=Y=Z: 1.07 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 octamer prechannel bound to full-length lethal factor
Entire | Name: Anthrax octamer prechannel bound to full-length lethal factor |
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Components |
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-Supramolecule #1: Anthrax octamer prechannel bound to full-length lethal factor
Supramolecule | Name: Anthrax octamer prechannel bound to full-length lethal factor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 852 kDa/nm |
-Macromolecule #1: Protective antigen
Macromolecule | Name: Protective antigen / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 82.511336 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR EDPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS ...String: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR EDPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS TSAGPTVPDR DNDGIPDSLE VEGYTVDVKN KRTFLSPWIS NIHEKKGLTK YKSSPEKWST ASDPYSDFEK VT GRIDGNV SPEANHPLVA AYPIVHVDME NIILSKNEDQ STQNTDSQTR TISKNTSTSR THTSEVHGNA EVHASFFDIG GSV SAGFSN SNSSTVAIDH SLSLAGERTW AETMGLNTAD TARLNANIRY VNTGTAPIYN VLPTTSLVLG KNQTLATIKA KENQ LSQIL APNNYYPSKN LAPIALNAQD DFSSTPITMN YNQFLELEKT KQLRLDTDQV YGNIATYNFE NGRVRVDTGS NWSEV LPQI QETTARIIFN GKDLNLVERR IAAVNPSDPL ETTKPDMTLK EALKIAFGFN EPNGNLQYQG KDITEFDFNF DQQTSQ NIK NQLAELNATN IYTVLDKIKL NAKMNILIRD KRFHYDRNNI AVGADESVVK EAHREVINSS TEGLLLNIDK DIRKILS GY IVEIEDTEGL KEVINDRYDM LNISSLRQDG KTFIDFKKYN DKLPLYISNP NYKVNVYAVT KENTIINPSE NGDTSTNG I KKILIFSKKG YEIG UniProtKB: Protective antigen |
-Macromolecule #2: Protective antigen
Macromolecule | Name: Protective antigen / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 82.639672 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR ENPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS ...String: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR ENPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS TSAGPTVPDR DNDGIPDSLE VEGYTVDVKN KRTFLSPWIS NIHEKKGLTK YKSSPEKWST ASDPYSDFEK VT GRIDKNV SPEARHPLVA AYPIVHVDME NIILSKNEDQ STQNTDSQTR TISKNTSTSR THTSEVHGNA EVHASFFDIG GSV SAGFSN SNSSTVAIDH SLSLAGERTW AETMGLNTAD TARLNANIRY VNTGTAPIYN VLPTTSLVLG KNQTLATIKA KENQ LSQIL APNNYYPSKN LAPIALNAQD DFSSTPITMN YNQFLELEKT KQLRLDTDQV YGNIATYNFE NGRVRVDTGS NWSEV LPQI QETTARIIFN GKDLNLVERR IAAVNPSKPL ETTKPDMTLK EALKIAFGFN EPNGNLQYQG KDITEFDFNF DQQTSQ NIK NQLAELNATN IYTVLDKIKL NAKMNILIRD KRFHYDRNNI AVGADESVVK EAHREVINSS TEGLLLNIDK DIRKILS GY IVEIEDTEGL KEVINDRYDM LNISSLRQDG KTFIDFKKYN DKLPLYISNP NYKVNVYAVT KENTIINPSE NGDTSTNG I KKILIFSKKG YEIG UniProtKB: Protective antigen |
-Macromolecule #3: Lethal factor
Macromolecule | Name: Lethal factor / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 90.356812 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYEPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ ...String: AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYEPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ KFLDVLNTIK NASDSDGQDL LFTNQLKEHP TDFSVEFLEQ NSNEVQEVFA KAFAYYIEPQ HRDVLQLYAP EA FNYMDKF NEQEINLSLE ELKDQRMLSR YEKWEKIKQH YQHWSDSLSE EGRGLLKKLQ IPIEPKKDDI IHSLSQEEKE LLK RIQIDS SDFLSTEEKE FLKKLQIDIR DSLSEEEKEL LNRIQVDSSN PLSEKEKEFL KKLKLDIQPY DINQRLQDTG GLID SPSIN LDVRKQYKRD IQNIDALLHQ SIGSTLYNKI YLYENMNINN LTATLGADLV DSTDNTKINR GIFNEFKKNF KYSIS SNYM IVDINERPAL DNERLKWRIQ LSPDTRAGYL ENGKLILQRN IGLEIKDVQI IKQSEKEYIR IDAKVVPKSK IDTKIQ EAQ LNINQEWNKA LGLPKYTKLI TFNVHNRYAS NIVESAYLIL NEWKNNIQSD LIKKVTNYLV DGNGRFVFTD ITLPNIA EQ YTHQDEIYEQ VHSKGLYVPE SRSILLHGPS KGVELRNDSE GFIHEFGHAV DDYAGYLLDK NQSDLVTNSK KFIDIFKE E GSNLTSYGRT NEAEFFAEAF RLMHSTDHAE RLKVQKNAPK TFQFINDQIK FIINS UniProtKB: Lethal factor |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: SO4 |
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Molecular weight | Theoretical: 96.063 Da |
Chemical component information | ![]() ChemComp-SO4: |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: 62.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |