+Open data
-Basic information
Entry | Database: PDB / ID: 6psn | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Anthrax toxin protective antigen channels bound to lethal factor | ||||||||||||
Components |
| ||||||||||||
Keywords | TRANSLOCASE / anthrax toxin / protective antigen / lethal factor | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||||||||
Authors | Hardenbrook, N.J. / Liu, S. / Zhou, K. / Zhou, Z.H. / Krantz, B.A. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Atomic structures of anthrax toxin protective antigen channels bound to partially unfolded lethal and edema factors. Authors: Nathan J Hardenbrook / Shiheng Liu / Kang Zhou / Koyel Ghosal / Z Hong Zhou / Bryan A Krantz / Abstract: Following assembly, the anthrax protective antigen (PA) forms an oligomeric translocon that unfolds and translocates either its lethal factor (LF) or edema factor (EF) into the host cell. Here, we ...Following assembly, the anthrax protective antigen (PA) forms an oligomeric translocon that unfolds and translocates either its lethal factor (LF) or edema factor (EF) into the host cell. Here, we report the cryo-EM structures of heptameric PA channels with partially unfolded LF and EF at 4.6 and 3.1-Å resolution, respectively. The first α helix and β strand of LF and EF unfold and dock into a deep amphipathic cleft, called the α clamp, which resides at the interface of two PA monomers. The α-clamp-helix interactions exhibit structural plasticity when comparing the structures of lethal and edema toxins. EF undergoes a largescale conformational rearrangement when forming the complex with the channel. A critical loop in the PA binding interface is displaced for about 4 Å, leading to the weakening of the binding interface prior to translocation. These structures provide key insights into the molecular mechanisms of translocation-coupled protein unfolding and translocation. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6psn.cif.gz | 714.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6psn.ent.gz | 592.4 KB | Display | PDB format |
PDBx/mmJSON format | 6psn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6psn_validation.pdf.gz | 984.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6psn_full_validation.pdf.gz | 1023.2 KB | Display | |
Data in XML | 6psn_validation.xml.gz | 104.8 KB | Display | |
Data in CIF | 6psn_validation.cif.gz | 160.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ps/6psn ftp://data.pdbj.org/pub/pdb/validation_reports/ps/6psn | HTTPS FTP |
-Related structure data
Related structure data | 20459MC 6uzbC 6uzdC 6uzeC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 63519.508 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: pagA, pag, pXO1-110, BXA0164, GBAA_pXO1_0164 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13423 #2: Protein | | Mass: 93904.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef, pXO1-107, BXA0172, GBAA_pXO1_0172 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P15917, anthrax lethal factor endopeptidase #3: Chemical | ChemComp-CA / Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Anthrax toxin protective antigen channels bound to lethal factor Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus anthracis (anthrax bacterium) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 62.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63807 / Symmetry type: POINT |