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- EMDB-20459: Anthrax toxin protective antigen channels bound to lethal factor -

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Basic information

Entry
Database: EMDB / ID: EMD-20459
TitleAnthrax toxin protective antigen channels bound to lethal factor
Map data
Sample
  • Complex: Anthrax toxin protective antigen channels bound to lethal factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Lethal factor
  • Ligand: CALCIUM IONCalcium
Keywordstranslocase / 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 / membrane / identical protein binding / 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
Protective antigen / Lethal factor
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsHardenbrook NJ / Liu S
Funding support United States, 3 items
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
DepositionJul 12, 2019-
Header (metadata) releaseJan 29, 2020-
Map releaseMar 4, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6psn
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20459.png

Downloads & links

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Map

FileDownload / File: emd_20459.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.019546645 - 0.07675552
Average (Standard dev.)-0.0000016830525 (±0.0037916696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z342.400342.400342.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0200.077-0.000

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Supplemental data

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Sample components

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Entire : Anthrax toxin protective antigen channels bound to lethal factor

EntireName: Anthrax toxin protective antigen channels bound to lethal factor
Components
  • Complex: Anthrax toxin protective antigen channels bound to lethal factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Lethal factor
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Anthrax toxin protective antigen channels bound to lethal factor

SupramoleculeName: Anthrax toxin protective antigen channels bound to lethal factor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)

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Macromolecule #1: Protective antigen

MacromoleculeName: Protective antigen / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 63.519508 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: STSAGPTVPD RDNDGIPDSL EVEGYTVDVK NKRTFLSPWI SNIHEKKGLT KYKSSPEKWS TASDPYSDFE KVTGRIDKNV SPEARHPLV AAYPIVHVDM ENIILSKNED QSTQNTDSQT RTISKNTSTS RTHTSEVHGN AEVHASFFDI GGSVSAGFSN S NSSTVAID ...String:
STSAGPTVPD RDNDGIPDSL EVEGYTVDVK NKRTFLSPWI SNIHEKKGLT KYKSSPEKWS TASDPYSDFE KVTGRIDKNV SPEARHPLV AAYPIVHVDM ENIILSKNED QSTQNTDSQT RTISKNTSTS RTHTSEVHGN AEVHASFFDI GGSVSAGFSN S NSSTVAID HSLSLAGERT WAETMGLNTA DTARLNANIR YVNTGTAPIY NVLPTTSLVL GKNQTLATIK AKENQLSQIL AP NNYYPSK NLAPIALNAQ DDFSSTPITM NYNQFLELEK TKQLRLDTDQ VYGNIATYNF ENGRVRVDTG SNWSEVLPQI QET TARIIF NGKDLNLVER RIAAVNPSDP LETTKPDMTL KEALKIAFGF NEPNGNLQYQ GKDITEFDFN FDQQTSQNIK NQLA ELNAT NIYTVLDKIK LNAKMNILIR DKRFHYDRNN IAVGADESVV KEAHREVINS STEGLLLNID KDIRKILSGY IVEIE DTEG LKEVINDRYD MLNISSLRQD GKTFIDFKKY NDKLPLYISN PNYKVNVYAV TKENTIINPS ENGDTSTNGI KKILIF SKK GYEIG

UniProtKB: Protective antigen

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Macromolecule #2: Lethal factor

MacromoleculeName: Lethal factor / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: anthrax lethal factor endopeptidase
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 93.904211 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNIKKEFIKV ISMSCLVTAI TLSGPVFIPL VQGAGGHGDV GMHVKEKEKN KDENKRKDEE RNKTQEEHLK EIMKHIVKIE VKGEEAVKK EAAEKLLEKV PSDVLEMYKA IGGKIYIVDG DITKHISLEA LSEDKKKIKD IYGKDALLHE HYVYAKEGYE P VLVIQSSE ...String:
MNIKKEFIKV ISMSCLVTAI TLSGPVFIPL VQGAGGHGDV GMHVKEKEKN KDENKRKDEE RNKTQEEHLK EIMKHIVKIE VKGEEAVKK EAAEKLLEKV PSDVLEMYKA IGGKIYIVDG DITKHISLEA LSEDKKKIKD IYGKDALLHE HYVYAKEGYE P VLVIQSSE DYVENTEKAL NVYYEIGKIL SRDILSKINQ PYQKFLDVLN TIKNASDSDG QDLLFTNQLK EHPTDFSVEF LE QNSNEVQ EVFAKAFAYY IEPQHRDVLQ LYAPEAFNYM DKFNEQEINL SLEELKDQRM LARYEKWEKI KQHYQHWSDS LSE EGRGLL KKLQIPIEPK KDDIIHSLSQ EEKELLKRIQ IDSSDFLSTE EKEFLKKLQI DIRDSLSEEE KELLNRIQVD SSNP LSEKE KEFLKKLKLD IQPYDINQRL QDTGGLIDSP SINLDVRKQY KRDIQNIDAL LHQSIGSTLY NKIYLYENMN INNLT ATLG ADLVDSTDNT KINRGIFNEF KKNFKYSISS NYMIVDINER PALDNERLKW RIQLSPDTRA GYLENGKLIL QRNIGL EIK DVQIIKQSEK EYIRIDAKVV PKSKIDTKIQ EAQLNINQEW NKALGLPKYT KLITFNVHNR YASNIVESAY LILNEWK NN IQSDLIKKVT NYLVDGNGRF VFTDITLPNI AEQYTHQDEI YEQVHSKGLY VPESRSILLH GPSKGVELRN DSEGFIHE F GHAVDDYAGY LLDKNQSDLV TNSKKFIDIF KEEGSNLTSY GRTNEAEFFA EAFRLMHSTD HAERLKVQKN APKTFQFIN DQIKFIINS

UniProtKB: Lethal factor

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 14 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 62.9 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6224

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 63807

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