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- PDB-6uzd: Anthrax toxin protective antigen channels bound to edema factor -

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Basic information

Entry
Database: PDB / ID: 6uzd
TitleAnthrax toxin protective antigen channels bound to edema factor
Components
  • Calmodulin-sensitive adenylate cyclase
  • Protective antigen
KeywordsTRANSLOCASE / anthrax toxin / protective antigen / edema factor
Function / homology
Function and homology information


symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / symbiont-mediated suppression of host MAPK cascade / 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 ...symbiont-mediated perturbation of host signal transduction pathway / symbiont-mediated cAMP intoxication of host cell / symbiont-mediated suppression of host MAPK cascade / 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 / host cell endosome membrane / adenylate cyclase activator activity / protein homooligomerization / metallopeptidase activity / toxin activity / calmodulin binding / host cell plasma membrane / extracellular region / ATP binding / metal ion binding / identical protein binding / membrane
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/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. / PA14/GLEYA domain / PA14 domain profile. / 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 domain / PA14 / PA14 domain / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
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: 3.4 Å
AuthorsHardenbrook, N.J. / Liu, S. / Zhou, K. / Zhou, Z.H. / Krantz, B.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R01GM071940/AI094386/DE025567 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)R21AI124020 United States
CitationJournal: 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
DepositionNov 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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  • Deposited structure unit
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  • EMDB-20957
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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: Calmodulin-sensitive adenylate cyclase
I: Calmodulin-sensitive adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)757,85423
Polymers757,2939
Non-polymers56114
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 82768.828 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P13423
#2: 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.: 2
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40136, adenylate cyclase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / 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 toxin protective antigen channels bound to edema factor
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 613 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
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72864 / Symmetry type: POINT

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