Structure of EccB3 dimer from the ESX-3 core complex

2024-10-16 REL PDBe PDBe PDBe 2019-08-05 2019-09-11 2019-10-09 2024-10-16 German Research Foundation Elite Network of Bavaria (N-BM-2013-246), Bavarian State Ministry of Science and the Arts Germany Spanish Ministry of Science, Innovation, and Universities SAF2017-82632-P o-funded by the European Regional Development Fund Spain European Regional Development Fund Y2018/BIO4747 co-funded by the Autonomous Region of Madrid Spain European Regional Development Fund P2018/NMT4443 co-funded by Autonomous Region of Madrid Spain European Union Horizon 2020, iNEXT (PID2907) , Grant number 653706 Spain Bavarian State Ministry of Science and the Arts Funding Organisation N-BM-2013-246 Germany Structure of EccB3 dimer from the ESX-3 core complex Rivera-Calzada A Famelis N Geibel S Llorca O Type VII Secretion System ESX-3 secretion system T7SS ESX-3 Mycobacterium smegmatis, MEMBRANE PROTEIN Famelis N Rivera-Calzada A Degliesposti G Wingender M Mietrach N Skehel JM Fernandez-Leiro R Bottcher B Schlosser A Llorca O Geibel S Architecture of the mycobacterial type VII secretion system. Nature UK 576 321 325 2019 31597161 doi:10.1038/s41586-019-1633-1 1476-4687 0006 NATUAS 6sgy FULLOVERLAP EccB3 dimeric structure from ESX-3/Type VII secretion system EccB3 dimeric structure from ESX-3/Type VII secretion system 0 1

The sample consists of four protein components, EccB3:EccC3:EccD3:EccE3 in a 1:1:2:1 stoichiometry Molecular weight of the complex without the amphipol micelle: 0.65 MDa

Mycolicibacterium smegmatis MC2 155 0.083 ESX-3 secretion system protein EccB3 Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) 0.042746754 2 Mycolicibacterium smegmatis MC2 155 LEVO NAILADRSTSALYVRVGEQLHPVLNLTSARLISGSPDNPTMVKTSEIDKFPRGNLLGIPGAPERMVQNAATDAEWTVCDA VGGANPGVTVIAGPLGADGERAAPLPPDHAVLVHSDAEPNPGDWLLWDGKRSPIDLADRAVTDALGLGGQALAPRPIAAG LFNAVPAAPALTAPVIPDAGAAPQFELSLPVPVGAVVVAYDADNTARYYAVLSDGLQPISPVLAAILRNTDSHGFAQPPR LGPDEVARTPMSRGLDTSAYPDNPVTLVEASAHPVTCAHWTKPSDAAESSLSVLSGAVLPLAEGLHTVDLVGAGAGGAAN RVALTPGTGYFVQTVGAEPGSPTAGSMFWVSDTGVRYGIDTAEDDKVVAALGLSTSPLPVPWSVLSQFAAGPALSRGDAL VAHDAVSTNPNSARMEASR A0QQ39 singleParticle particle 0.3 8.0

30 mM Hepes pH 8.0, 150 mM NaCl

ETHANE 100 278 FEI VITROBOT MARK IV

Blotting time: 3s Blotting force: -10.

bound to Amphipol A8-35

FEI TITAN KRIOS SPOT SCAN BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.6 2.6 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) COUNTING 11903 50.0

Images acquired as 55 frames movies at a calibrated magnification of 1.0635 Angs/px

Images were collected in counting mode

2066007 C2 4.6 FSC 0.143 CUT-OFF RELION

Particles were extracted centred at extracellular density instead than in the centre of mass in order to improve the resolution in that distal region. Extra density not corresponding to the EccB3 dimer was subtracted

55342 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION emd_10188.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 304 304 304 0 0 0 304 304 304 323.30402 323.30402 323.30402 90.0 90.0 90.0 X Y Z -0.048456762 0.0922983 0.000056797973 0.0018579063 1.0635 1.0635 1.0635 0.03 AUTHOR ::::EMDATABANK.org::::EMD-10188:::: EccB3 dimer. 3X3M A 100-518 PDB experimental model AB INITIO MODEL

Two copies of the periplasmic domain of a EccB3 homology model (based on pdb 3X3M) were fitted into the density and then morphing was performed using PHENIX Real-Space Refinement.

Map correlation coefficient REAL