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- PDB-6wjj: Anthrax octamer prechannel bound to full-length lethal factor -

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Basic information

Entry
Database: PDB / ID: 6wjj
TitleAnthrax octamer prechannel bound to full-length lethal factor
Components
  • (Protective antigen) x 2
  • Lethal factor
KeywordsTRANSLOCASE / anthrax toxin / protective antigen / lethal factor / octamer
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 ...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
Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain ...Anthrax toxin lethal factor, central domain / Anthrax toxin lethal factor, middle domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, lethal/endema factor / : / Anthrax toxin lethal factor (ATLF)-like domain profile. / Anthrax toxin, lethal/endema factor, N-/C-terminal / Anthrax toxin lethal factor, N- and C-terminal domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Lethal factor / Protective antigen / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhou, K. / Hardenbrook, N.J. / Liu, S. / Cui, Y.X. / Krantz, B.A. / Zhou, Z.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)R01GM071940/AI094386/DE025567 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)R21AI124020 United States
CitationJournal: 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
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Protective antigen
B: Protective antigen
L: Lethal factor
C: Protective antigen
F: Protective antigen
I: Lethal factor
D: Protective antigen
G: Protective antigen
J: Lethal factor
E: Protective antigen
H: Protective antigen
K: Lethal factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,023,31836
Polymers1,022,03112
Non-polymers1,28724
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 12 molecules ACDEBFGHLIJK

#1: Protein
Protective antigen / PA / Anthrax toxins translocating protein / PA-83 / PA83


Mass: 82511.336 Da / Num. of mol.: 4
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13423
#2: Protein
Protective antigen / PA / Anthrax toxins translocating protein / PA-83 / PA83


Mass: 82639.672 Da / Num. of mol.: 4
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13423
#3: Protein
Lethal factor


Mass: 90356.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: lef
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I3XID8, UniProt: P15917*PLUS

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Non-polymers , 3 types, 24 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Anthrax octamer prechannel bound to full-length lethal factor
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 852 kDa/nm / Experimental value: YES
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 62.9 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2Leginon2image acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11RELION3initial Euler assignment
12RELION3final Euler assignment
13RELION3classification
14RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23839 / Symmetry type: POINT

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