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- PDB-6vra: Anthrax octamer prechannel bound to full-length edema factor -

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Basic information

Entry
Database: PDB / ID: 6vra
TitleAnthrax octamer prechannel bound to full-length edema factor
Components
  • (Protective antigen) x 2
  • Calmodulin-sensitive adenylate cyclase
KeywordsTRANSLOCASE / 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 / negative regulation of MAPK cascade / 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 / negative regulation of MAPK cascade / Uptake and function of anthrax toxins / catalytic complex / small molecule binding / host cell endosome membrane / protein homooligomerization / metallopeptidase activity / toxin activity / calmodulin binding / host cell plasma membrane / extracellular region / ATP binding / membrane / identical protein binding / metal ion binding
Similarity search - Function
: / Oedema factor (EF), alpha-helical domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Anthrax toxin, lethal/endema factor ...: / Oedema factor (EF), alpha-helical domain / Protective antigen domain 4 / : / Anthrax protective antigen, immunoglobulin-like domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / 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
Similarity search - Domain/homology
Protective antigen / Calmodulin-sensitive adenylate cyclase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 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
DepositionFeb 7, 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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Assembly

Deposited unit
A: Protective antigen
B: Protective antigen
C: Protective antigen
D: Protective antigen
E: Protective antigen
F: Protective antigen
G: Protective antigen
H: Protective antigen
I: Calmodulin-sensitive adenylate cyclase
J: Calmodulin-sensitive adenylate cyclase
K: Calmodulin-sensitive adenylate cyclase
L: Calmodulin-sensitive adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,017,06828
Polymers1,016,42612
Non-polymers64116
Water00
1


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

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Components

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


Mass: 82511.336 Da / Num. of mol.: 4 / Mutation: K245G, R252N
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
Protective antigen / PA / Anthrax toxins translocating protein / PA-83 / PA83


Mass: 82639.672 Da / Num. of mol.: 4 / Mutation: D512K
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
#3: Protein
Calmodulin-sensitive adenylate cyclase / ATP pyrophosphate-lyase / Adenylyl cyclase / Anthrax edema toxin adenylate cyclase component / ...ATP pyrophosphate-lyase / Adenylyl cyclase / Anthrax edema toxin adenylate cyclase component / Edema factor / EF


Mass: 88955.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: cya, pXO1-122, BXA0141, GBAA_pXO1_0142 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40136, adenylate cyclase
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
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 edema factor
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 860 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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78465 / Symmetry type: POINT

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