ESX-3 core complex centred at the cytoplasmic region, conformation 1.

2019-12-25 REL PDBe PDBe PDBe 2019-08-05 2019-10-09 2019-10-09 2019-12-25 German Research Foundation Elite Network of Bavaria (N-BM-2013-246), Bavarian State Ministry of Science and the Arts Germany European Regional Development Fund Y2018/BIO4747 co-funded by the Autonomous Region of Madrid Spain Spanish Ministry of Science, Innovation, and Universities SAF2017-82632-P o-funded by the European Regional Development Fund Spain European Union Horizon 2020, iNEXT (PID2907) , Grant number 653706 Spain European Regional Development Fund P2018/NMT4443 co-funded by Autonomous Region of Madrid Spain Bavarian State Ministry of Science and the Arts Funding Organisation N-BM-2013-246 Germany ESX-3 core complex centred at the cytoplasmic region, conformation 1. Rivera-Calzada A Famelis N Geibel S Llorca O 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 EMD-10189 associated EM volume ESX-3 core complex, conformation 1 ESX-3 core complex, conformation 1 0 1 2 3 4

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 Mycolicibacterium smegmatis MC2 155 0.65 EccB3 Mycolicibacterium smegmatis MC2 155 Mycolicibacterium smegmatis MC2 155 LEVO MTGPVNPDDRRSFSSRTPVNENPDGVQYRRGFVTRHQVSGWRFVMRRIASGVALHDTRML VDPLRTQSRAVLTGALILVTGLVGCFIFSLFRPGGVPGNNAILADRSTSALYVRVGEQLH PVLNLTSARLISGSPDNPTMVKTSEIDKFPRGNLLGIPGAPERMVQNAATDAEWTVCDAV GGANPGVTVIAGPLGADGERAAPLPPDHAVLVHSDAEPNPGDWLLWDGKRSPIDLADRAV TDALGLGGQALAPRPIAAGLFNAVPAAPALTAPVIPDAGAAPQFELSLPVPVGAVVVAYD ADNTARYYAVLSDGLQPISPVLAAILRNTDSHGFAQPPRLGPDEVARTPMSRGLDTSAYP DNPVTLVEASAHPVTCAHWTKPSDAAESSLSVLSGAVLPLAEGLHTVDLVGAGAGGAANR VALTPGTGYFVQTVGAEPGSPTAGSMFWVSDTGVRYGIDTAEDDKVVAALGLSTSPLPVP WSVLSQFAAGPALSRGDALVAHDAVSTNPNSARMEASR EccD3 Mycolicibacterium smegmatis MC2 155 Mycolicibacterium smegmatis MC2 155 LEVO MASWSHPQFEKGSMSENTVMPIVRVAVLAAGDDGGRLTEMALPSELPLREILPAVQRIVQPARENDGAADPAAAPNPVRLSLAPIGGAPFSLDATLDTVGVVDGDLLALQAVPSGPPAPRIVEDIADAAVIFSEARRRQWGPTHIARGAALALIGLILVGTGLSVAHRVITGDLLGQFIVSGIALATVIAALAVRNRSAVLATSLAVTALVPVAAAFALGVPGDFGAPNVLLAAAGVAAWSLISMAGSPDDRGIAVFTATAVTGVGVLLVAGAASLWVISSDVIGCALVLLGLIVTVQAAQLSAMWARFPLPVIPAPGDPTPAARPLSVLADLPRRVRVSQAHQTGVIAAGVLLGVAGSVALVSSANASPWAWYIVVAAAAGAALRARVWDSAACKAWLLGHSYLLAVALLVAFVIGDRYQAALWALAALAVLVLVWIVAALNPKIASPDTYSLPMRRMVGFLATGLDASLIPVMALLVGLFSLVLDR EccC3 Mycolicibacterium smegmatis MC2 155 Mycolicibacterium smegmatis MC2 155 LEVO MSRLIFEHQRRLTPPTTRKGTITIEPPPQLPRVVPPSLLRRVLPFLIVILIVGMIVALFA TGMRLISPTMLFFPFVLLLAATALYRGGDNKMRTEEVDAERADYLRYLSVVRDNVRAHAA EQRAALEWSHPEPEVLATIPGTRRQWERDPRDRDFLVLRAGRHDVPLDAALKVKDTADEI DLEPVAHSALRGLLDVQRTVRDAPTGLDVAKLARITVIGEADEARAAIRAWIAQAVTWHD PTMLGVALAAPDLESGDWSWLKWLPHVDVPNEADGVGPARYLTTSTAELRERLAPALADR PLFPAESGAALKHLLVVLDDPDADPDDIARKPGLTGVTVIHRTTELPNREQYPDPERPIL RVADGRIERWQVGGWQPCVDVADAMSAAEAAHIARRLSRWDSNPGYIRSTSTGSATFTTL LGIPDASALDVASLWAPRPRDEELRVPIGVTSTGEPLYFDLKDEAEGGMGPHGLMIGMTG SGKSQTLMSILLSLLTTHPADRLIVIYADFKGEAGADIFRHFPQVVAVISNMAEKRSLAD RFADTLRGEVARREQILKEAGRRVQGSAFNSVAEYESAIAAGHDLPPMPTLFVVADEFTL MLAEHPEYADLFDYVARKGRSFRIHLLFASQTLDVGRIKDIDKNTSYRIGLKVASPSISR QIIGVEDAYHIESGREHKGEGFLVPAPGAVPIKFRSTYVDGIYDPPRAEKSIVVHALPQP QVFTAGRVEPEPDTVIATGDVEVHTAPPRKLIATIGDQLAAYGPKAPQLWLPPLDEPIAL ADVLAGADVEPGQLRWPLGEIDKPFEMRRDVLVYDAHTAAANVLIHGGPRSGKSTALQAF VLSAAALHSPRAITFYCLDYGGGKLADLADLAHVGSVATPLEPERIRRTFGELEQLLRAR QRQGAVNRTGSYTDGYGEVFLVIDNLYAFSRDNTDTFNTRNPLLAKVTELANSGLAYGIH VVITTPNWLEVPLAMRDGLGLRLELKLHDSHDSIVRVAGALRRPADSVPADQPGRGLTMA AEHFLFAEPALSDIAVINARYPGVSAPPVRLLPTDLSPDALAPLYPAPETVVIGQREEDL APVAVDFANHPLLMVFGDSKSGKTTLLRHIIRTVRENSTPDQVAFTVIDRRLHLVDEPLF PDNEYTANIDRVLPAMLGLSALIEKRRPPAGLSAQELSRWTYTGHTHYLIVDDVDQIPDT PAVSGPFVGQRPWTNIVGLLAEAADLGLRVIVTARATGSAHAVMTAPLLRRLNDLQATTL MLSGNPTDSGKIRGHRFARFPAGRGLLLTDTDTPDHIQLVNPLGDAALSGNIGNNGNHNR GGEYRGSMGGSHHHHHH EccE3 Mycolicibacterium smegmatis MC2 155 Mycolicibacterium smegmatis MC2 155 LEVO MTARIALASLFVVAAVLAQPWQTTTQRWVLGVSIAAVIVLLAWWKGMFLTTRIGRALAMV RRNRAEDTVETDAHRATVVLRVDPAAPAQLPVVVGYLDRYGITCDKVRITHRDAGGTRRS WISLTVDAVDNLAALQARSARIPLQDTTEVVGRRLADHLREQGWTVTVVEGVDTPLPVSG KETWRGVADDAGVVAAYRVKVDDRLDEVLAEIGHLPAEETWTALEFTGSPAEPLLTVCAA VRTSDRPAAKAPLAGLTPARGRHRPALAALNPLSTERLDGTAVPLPAVVRTSVKGSVEHE AAQEAGHPA singleParticle particle 0.3 8

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

Particles were extracted centred at the distal cytoplasmic tip instead than in the centre of mass in order to improve the resolution in that distal region.

Gctf C1 5.4 FSC 0.143 CUT-OFF RELION 80173 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION emd_10189.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 442.41602 442.41602 442.41602 90.0 90.0 90.0 X Y Z -0.037227653 0.08501123 -0.00000052725 0.0022724236 1.0635 1.0635 1.0635 0.0085 AUTHOR ::::EMDATABANK.org::::EMD-10189:::: ESX-3 core dimer centred at the cytoplasmic region, conformation 1. 4NH0 B 401-772 RIGID BODY FIT

A homology model based on pdb 4NH0 was created using Phyre2 and fitted into the density using Chimera.

Map correlation coefficient