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- EMDB-21694: Anthrax octamer prechannel bound to full-length lethal factor -

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Basic information

Entry
Database: EMDB / ID: EMD-21694
TitleAnthrax octamer prechannel bound to full-length lethal factor
Map data
Sample
  • Complex: Anthrax octamer prechannel bound to full-length lethal factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Protective antigen
    • Protein or peptide: Lethal factor
  • Ligand: CALCIUM ION
  • Ligand: SULFATE ION
  • Ligand: ZINC ION
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 / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / 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 / Uptake and function of anthrax toxins / negative regulation of MAPK cascade / 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/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like domain profile. ...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/endema factor, N-/C-terminal / : / Anthrax toxin lethal factor, N- and C-terminal domain / Anthrax toxin lethal factor (ATLF)-like 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/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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhou K / Hardenbrook NJ
Funding support United States, 3 items
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, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wjj
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21694.png

Downloads & links

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Map

FileDownload / File: emd_21694.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. 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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.081010796 - 0.15427679
Average (Standard dev.)-0.000034046996 (±0.0060686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z321.000321.000321.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0810.154-0.000

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Supplemental data

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Sample components

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Entire : Anthrax octamer prechannel bound to full-length lethal factor

EntireName: Anthrax octamer prechannel bound to full-length lethal factor
Components
  • Complex: Anthrax octamer prechannel bound to full-length lethal factor
    • Protein or peptide: Protective antigen
    • Protein or peptide: Protective antigen
    • Protein or peptide: Lethal factor
  • Ligand: CALCIUM ION
  • Ligand: SULFATE ION
  • Ligand: ZINC ION

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Supramolecule #1: Anthrax octamer prechannel bound to full-length lethal factor

SupramoleculeName: Anthrax octamer prechannel bound to full-length lethal factor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 852 kDa/nm

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Macromolecule #1: Protective antigen

MacromoleculeName: Protective antigen / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 82.511336 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR EDPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS ...String:
QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR EDPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS TSAGPTVPDR DNDGIPDSLE VEGYTVDVKN KRTFLSPWIS NIHEKKGLTK YKSSPEKWST ASDPYSDFEK VT GRIDGNV SPEANHPLVA AYPIVHVDME NIILSKNEDQ STQNTDSQTR TISKNTSTSR THTSEVHGNA EVHASFFDIG GSV SAGFSN SNSSTVAIDH SLSLAGERTW AETMGLNTAD TARLNANIRY VNTGTAPIYN VLPTTSLVLG KNQTLATIKA KENQ LSQIL APNNYYPSKN LAPIALNAQD DFSSTPITMN YNQFLELEKT KQLRLDTDQV YGNIATYNFE NGRVRVDTGS NWSEV LPQI QETTARIIFN GKDLNLVERR IAAVNPSDPL ETTKPDMTLK EALKIAFGFN EPNGNLQYQG KDITEFDFNF DQQTSQ NIK NQLAELNATN IYTVLDKIKL NAKMNILIRD KRFHYDRNNI AVGADESVVK EAHREVINSS TEGLLLNIDK DIRKILS GY IVEIEDTEGL KEVINDRYDM LNISSLRQDG KTFIDFKKYN DKLPLYISNP NYKVNVYAVT KENTIINPSE NGDTSTNG I KKILIFSKKG YEIG

UniProtKB: Protective antigen

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Macromolecule #2: Protective antigen

MacromoleculeName: Protective antigen / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 82.639672 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR ENPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS ...String:
QENRLLNESE SSSQGLLGYY FSDLNFQAPM VVTSSTTGDL SIPSSELENI PSENQYFQSA IWSGFIKVKK SDEYTFATSA DNHVTMWVD DQEVINKASN SNKIRLEKGR LYQIKIQYQR ENPTEKGLDF KLYWTDSQNK KEVISSDNLQ LPELKQKSSN S LEVLFQGS TSAGPTVPDR DNDGIPDSLE VEGYTVDVKN KRTFLSPWIS NIHEKKGLTK YKSSPEKWST ASDPYSDFEK VT GRIDKNV SPEARHPLVA AYPIVHVDME NIILSKNEDQ STQNTDSQTR TISKNTSTSR THTSEVHGNA EVHASFFDIG GSV SAGFSN SNSSTVAIDH SLSLAGERTW AETMGLNTAD TARLNANIRY VNTGTAPIYN VLPTTSLVLG KNQTLATIKA KENQ LSQIL APNNYYPSKN LAPIALNAQD DFSSTPITMN YNQFLELEKT KQLRLDTDQV YGNIATYNFE NGRVRVDTGS NWSEV LPQI QETTARIIFN GKDLNLVERR IAAVNPSKPL ETTKPDMTLK EALKIAFGFN EPNGNLQYQG KDITEFDFNF DQQTSQ NIK NQLAELNATN IYTVLDKIKL NAKMNILIRD KRFHYDRNNI AVGADESVVK EAHREVINSS TEGLLLNIDK DIRKILS GY IVEIEDTEGL KEVINDRYDM LNISSLRQDG KTFIDFKKYN DKLPLYISNP NYKVNVYAVT KENTIINPSE NGDTSTNG I KKILIFSKKG YEIG

UniProtKB: Protective antigen

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Macromolecule #3: Lethal factor

MacromoleculeName: Lethal factor / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus anthracis (anthrax bacterium)
Molecular weightTheoretical: 90.356812 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYEPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ ...String:
AGGHGDVGMH VKEKEKNKDE NKRKDEERNK TQEEHLKEIM KHIVKIEVKG EEAVKKEAAE KLLEKVPSDV LEMYKAIGGK IYIVDGDIT KHISLEALSE DKKKIKDIYG KDALLHEHYV YAKEGYEPVL VIQSSEDYVE NTEKALNVYY EIGKILSRDI L SKINQPYQ KFLDVLNTIK NASDSDGQDL LFTNQLKEHP TDFSVEFLEQ NSNEVQEVFA KAFAYYIEPQ HRDVLQLYAP EA FNYMDKF NEQEINLSLE ELKDQRMLSR YEKWEKIKQH YQHWSDSLSE EGRGLLKKLQ IPIEPKKDDI IHSLSQEEKE LLK RIQIDS SDFLSTEEKE FLKKLQIDIR DSLSEEEKEL LNRIQVDSSN PLSEKEKEFL KKLKLDIQPY DINQRLQDTG GLID SPSIN LDVRKQYKRD IQNIDALLHQ SIGSTLYNKI YLYENMNINN LTATLGADLV DSTDNTKINR GIFNEFKKNF KYSIS SNYM IVDINERPAL DNERLKWRIQ LSPDTRAGYL ENGKLILQRN IGLEIKDVQI IKQSEKEYIR IDAKVVPKSK IDTKIQ EAQ LNINQEWNKA LGLPKYTKLI TFNVHNRYAS NIVESAYLIL NEWKNNIQSD LIKKVTNYLV DGNGRFVFTD ITLPNIA EQ YTHQDEIYEQ VHSKGLYVPE SRSILLHGPS KGVELRNDSE GFIHEFGHAV DDYAGYLLDK NQSDLVTNSK KFIDIFKE E GSNLTSYGRT NEAEFFAEAF RLMHSTDHAE RLKVQKNAPK TFQFINDQIK FIINS

UniProtKB: Lethal factor

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 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
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6224

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23839
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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