2024-05-01 REL PDBe PDBe PDBe 2020-07-29 2020-09-02 2020-09-02 2024-05-01 European Research Council (ERC) 615984 Germany Fully-loaded anthrax lethal toxin in its heptameric pre-pore state, in which the third lethal factor is masked out (PA7LF3-masked) Quentin D Antoni C anthrax lethal toxin, fully-loaded pre-pore state, membrane translocase, cytotoxic substrate, TOXIN Antoni C Quentin D Lang AE Aktories K Gatsogiannis C Raunser S Cryo-EM structure of the fully-loaded asymmetric anthrax lethal toxin in its heptameric pre-pore state. Plos Pathog. US 16 e1008530 e1008530 2020 32810181 doi:10.1371/journal.ppat.1008530 1553-7374 6zxj FULLOVERLAP Fully-loaded anthrax lethal toxin in its heptameric pre-pore state Fully-loaded anthrax lethal toxin in its heptameric pre-pore state 0 1 2
Heptameric pre-pores of proteolytically-acitivated protective antigen were loaded with excess of LFs to create the PA7LF3 complexes. The flexible third LF is masked out in the final reconstruction to boost the resolution of the rest of the complex.
0.093 Protective antigen 1 1
The trypsin-activated 63 kDa fragments assemble into a hepatameric pre-pore
Bacillus anthracis Lethal factor 1 2
Three LF molecules crown the heptameric PA ring. The density corresponding to the third LF is masked out in the reconstruction.
Bacillus anthracis Protective antigen Bacillus anthracis 0.08567992999999999 7 Escherichia coli BL21(DE3) LEVO MGHHHHHHHHHHSSGHIDDDDKHMEVKQENRLLNESESSSQGLLGYYFSDLNFQAPMVVTSSTTGDLSIPSSELENIPSE NQYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIKIQYQRENPTEKGLDFKLYW TDSQNKKEVISSDNLQLPELKQKSSNSRKKRSTSAGPTVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGL TKYKSSPEKWSTASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTRTISKNTSTS RTHTSEVHGNAEVHASFFDIGGSVSAGFSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYVNTGTAPIYN VLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDFSSTPITMNYNQFLELEKTKQLRLDTDQVY GNIATYNFENGRVRVDTGSNWSEVLPQIQETTARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEP NGNLQYQGKDITEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGADESVVKEAH REVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISSLRQDGKTFIDFKKYNDKLPLYISNPNYKV NVYAVTKENTIINPSENGDTSTNGIKKILIFSKKGYEIG Q68GS1 Lethal factor Bacillus anthracis 0.09390421099999999 2 Bacillus anthracis LEVO MNIKKEFIKVISMSCLVTAITLSGPVFIPLVQGAGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIE VKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEP VLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLE QNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQRMLARYEKWEKIKQHYQHWSDSLSE EGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNP LSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLT ATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGL EIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWK NNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHE FGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFIN DQIKFIINS P15917 3.4.24.83 singleParticle particle 0.06 8.5 20.0 Tris-HCl Tris hydrochloride 150.0 NaCl sodium chloride Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE AIR ETHANE 95 286 GATAN CRYOPLUNGE 3
4 uL sample was applied to grid (with 2 nm additional carbon layer) and incubated for 45 s prior blotting..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.2 2.6 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 5238 15.0 74.4 1 382000 1TZO
A composite crystal structure was generated, based on 1TZO for the heptameric PA ring, 1J7N (full body of LF) and 3KWV (N-terminal part of LF) for the three LF molecules. This density was converted into an electron density map, filtered to 30 A and served as initial reference in the 3D refinement.
 1J7N
A composite crystal structure was generated, based on 1TZO for the heptameric PA ring, 1J7N (full body of LF) and 3KWV (N-terminal part of LF) for the three LF molecules. This density was converted into an electron density map, filtered to 30 A and served as initial reference in the 3D refinement.
 C1 BACK PROJECTION 3.5 FSC 0.143 CUT-OFF SPHIRE 210000 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD SPHIRE SPHIRE emd_11522.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 336 336 336 0 0 0 336 336 336 359.52002 359.52002 359.52002 90.0 90.0 90.0 X Y Z -1.08765 1.9266713 0.0011153694 0.031776376 1.07 1.07 1.07 0.1 AUTHOR PA7LF3 complex, with the third lethal factor (3-LF) masked out. 3HVD A PDB experimental model 1J7N A PDB experimental model FLEXIBLE FIT
The protective antigen (PA) monomer from 3HVD was placed seven times into the density corresponding to the heptameric PA ring using the rigid-body fit in Chimera. Two copies of the monomeric lethal factor (LF) from 1J7N were fitted similarly into the corresponding LF density located atop of the PA7 ring. The resulting model was then flexibly fitted using iMODFIT. The model was further refined in iterative rounds of phenix and coot. Unresolved regions were deleted and side chain information was removed for less well-defined regions.