+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21365 | ||||||||||||
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Title | Anthrax octamer prechannel bound to full-length edema factor | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | translocase / anthrax toxin / protective antigen / edema factor / octamer | ||||||||||||
Function / homology | Function and homology information positive regulation of apoptotic process in another organism / : / calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins / catalytic complex ...positive regulation of apoptotic process in another organism / : / calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / host cell cytosol / small molecule binding / Uptake and function of anthrax toxins / catalytic complex / negative regulation of MAPK cascade / host cell endosome membrane / protein homooligomerization / metallopeptidase activity / toxin activity / calmodulin binding / host cell plasma membrane / extracellular region / ATP binding / 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 | Zhou K / Hardenbrook NJ | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Structure / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21365.map.gz | 96.4 MB | EMDB map data format | |
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Header (meta data) | emd-21365-v30.xml emd-21365.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_21365.png | 216.3 KB | ||
Filedesc metadata | emd-21365.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21365 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21365 | HTTPS FTP |
-Validation report
Summary document | emd_21365_validation.pdf.gz | 562.3 KB | Display | EMDB validaton report |
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Full document | emd_21365_full_validation.pdf.gz | 561.8 KB | Display | |
Data in XML | emd_21365_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_21365_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21365 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21365 | HTTPS FTP |
-Related structure data
Related structure data | 6vraMC 6wjjC 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_21365.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Anthrax octamer prechannel bound to full-length edema factor
Entire | Name: Anthrax octamer prechannel bound to full-length edema factor |
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Components |
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-Supramolecule #1: Anthrax octamer prechannel bound to full-length edema factor
Supramolecule | Name: Anthrax octamer prechannel bound to full-length edema factor type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 860 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: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 82.511336 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 82.639672 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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: Calmodulin-sensitive adenylate cyclase
Macromolecule | Name: Calmodulin-sensitive adenylate cyclase / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: adenylate cyclase |
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Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
Molecular weight | Theoretical: 88.955578 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNEHYTESDI KRNHKTEKNK TEKEKFKDSI NNLVKTEFTN ETLDKIQQTQ DLLKKIPKDV LEIYSELGGE IYFTDIDLVE HKELQDLSE EEKNSMNSRG EKVPFASRFV FEKKRETPKL IINIKDYAIN SEQSKEVYYE IGKGISLDII SKDKSLDPEF L NLIKSLSD ...String: MNEHYTESDI KRNHKTEKNK TEKEKFKDSI NNLVKTEFTN ETLDKIQQTQ DLLKKIPKDV LEIYSELGGE IYFTDIDLVE HKELQDLSE EEKNSMNSRG EKVPFASRFV FEKKRETPKL IINIKDYAIN SEQSKEVYYE IGKGISLDII SKDKSLDPEF L NLIKSLSD DSDSSDLLFS QKFKEKLELN NKSIDINFIK ENLTEFQHAF SLAFSYYFAP DHRTVLELYA PDMFEYMNKL EK GGFEKIS ESLKKEGVEK DRIDVLKGEK ALKASGLVPE HADAFKKIAR ELNTYILFRP VNKLATNLIK SGVATKGLNV HGK SSDWGP VAGYIPFDQD LSKKHGQQLA VEKGNLENKK SITEHEGEIG KIPLKLDHLR IEELKENGII LKGKKEIDNG KKYY LLESN NQVYEFRISD ENNEVQYKTK EGKITVLGEK FNWRNIEVMA KNVEGVLKPL TADYDLFALA PSLTEIKKQI PQKEW DKVV NTPNSLEKQK GVTNLLIKYG IERKPDSTKG TLSNWQKQML DRLNEAVKYT GYTGGDVVNH GTEQDNEEFP EKDNEI FII NPEGEFILTK NWEMTGRFIE KNITGKDYLY YFNRSYNKIA PGNKAYIEWT DPITKAKINT IPTSAEFIKN LSSIRRS SN VGVYKDSGDK DEFAKKESVK KIAGYLSDYY NSANHIFSQE KKRKISIFRG IQAYNEIENV LKSKQIAPEY KNYFQYLK E RITNQVQLLL THQKSNIEFK LLYKQLNFTE NETDNFEVFQ KIIDEK UniProtKB: Calmodulin-sensitive adenylate cyclase |
-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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |