2025-08-13 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-06-05 2025-08-13 2025-08-13 2025-08-13 Wellcome Trust 223103/Z/21/Z United Kingdom European Research Council (ERC) 742210 European Union Wellcome Trust 222451/Z/21/Z United Kingdom M.tuberculosis MmpS5L5-acpM complex Fountain AJ Luisi BF Ramakrishnan L Drug efflux, RND transporter, Tuberculosis, MEMBRANE PROTEIN Fountain AJ Bohning J McLaughlin SH Morgan TE Edelstein PH Troll M Lamers MH Bharat TAM Luisi BF Ramakrishnan L Structural and functional analysis of the Mycobacterium tuberculosis MmpS5L5 efflux pump presages a pathway to increased bedaquiline resistance. Biorxiv US 2025 40667120 doi:10.1101/2025.06.24.661325 2692-8205 9rfu FULLOVERLAP EMDB EMD-53941 associated EM volume
M.tuberculosis MmpS5L5-acpM complex
 Trimeric M.tuberculosis MmpS5L5-acpM complex Trimeric M.tuberculosis MmpS5L5-acpM complex 0 1 2 3 Mycobacterium tuberculosis 411.9 Siderophore export accessory protein MmpS5 Mycobacterium tuberculosis H37Rv 0.0034572469999999997
M.tuberculosis MmpS5
3 Mycolicibacterium smegmatis MC2 155 LEVO SIGTLKRAWIPLLILVVVAIAGFTVQRIRTF P9WJS7 Siderophore exporter MmpL5 Mycobacterium tuberculosis 0.079180367
M.tuberculosis MmpL5 with deletion of residues 494-687. Fused to a C-terminal GFP-FLAG tag,M.tuberculosis MmpL5 with deletion of residues 494-687. Fused to a C-terminal GFP-FLAG tag
3 Mycolicibacterium smegmatis MC2 155 LEVO ARPFIPRMIRTFAVPIILGWLVTIAVLNVTVPQLETVGQIQAVSMSPDAAPSMISMKHIGKVFEEGDSDSAAMIVLEGQR PLGDAAHAFYDQMIGRLQADTTHVQSLQDFWGDPLTATGAQSSDGKAAYVQVKLAGNQGESLANESVEAVKTIVERLAPP PGVKVYVTGSAALVADQQQAGDRSLQVIEAVTFTVIIVMLLLVYRSIITSAIMLTMVVLGLLATRGGVAFLGFHRIIGLS TFATNLLVVLAIAAATDYAIFLIGRYQEARGLGQDRESAYYTMFGGTAHVVLGSGLTIAGATFCLSFTRLPYFQTLGVPL AIGMVIVVAAALTLGPAIIAVTSRFGKLLEPKRMARVRGWRKVGAAIVRWPGPILVGAVALALVGLLTLPGYRTNYNDRN YLPADLPANEGYAAAERHFSQARMNPEVLMVESDHDMRNSADFLVINKIAKAIFAVEGISRVQAITRPDGKPIESFYLPP EVFDNPDFQRGLEQFLSPDGHAVRFIISHEGDPMSQAGIARIAKIKTAAKEAIKGTPLEGSAIYLGGTAAMFKDLSDGNT YDLMIAGISALCLIFIIMLITTRSVVAAAVIVGTVVLSLGASFGLSVLIWQHILGIELHWLVLAMAVIILLAVGADYNLL LVARLKEEIHAGINTGIIRAMGGSGSVVTAAGLVFAFTMMSFAVSELTVMAQVGTTIGMGLLFDTLIVRSFMTPSIAALL GKWFWWPQVVRQRPIPQPW P9WJV1 P9WJV1 Meromycolate extension acyl carrier protein Mycolicibacterium smegmatis MC2 155 mc2 155 0.008808763
M.smegmatis acpM post-translationally modified with a phosphopantethiene group on Ser41.
3 LEVO ATQEEIIAGLAEIIEEVTGIEPSEVTPEKSFVDDLDID(4HH)LSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYIQ KL A0R0B3 (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate 0.00074605 3 L9Q singleParticle particle 2.2 8.0 150.0 NaCl Sodium chloride 50.0 HEPES 0.004 LMNG
50 mM HEPES pH 8.0, 150 mM NaCl, 0.004% LMNG
 UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE AIR 0.02
Edwards S150B glow discharger
 ETHANE 100 277 FEI VITROBOT MARK IV
This protein preparation contains both monomeric MmpL5-AcpM complexes, and a small subset of trimeric MmpS5L5-AcpM complexes in LMNG.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 2.2 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 1 6769 6.2 80.0
Images were collected at 0, 20 and 40 degree tilt, approximately equal numbers of movies for each tilt value.
 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 C1 3.3 FSC 0.143 CUT-OFF cryoSPARC 4.6.2 27426 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 MAXIMUM LIKELIHOOD cryoSPARC 4.6.2 emd_53941.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 382.0 382.0 382.0 90.0 90.0 90.0 X Y Z -0.0784335 0.16997784 0.00020318087 0.0046085594 0.955 0.955 0.955 0.03 AUTHOR Unsharpened cryo-EM map of M.tuberculosis MmpS5L5-acpM complex. AlphaFold in silico model
AlphaFold2 prediction of full-length MmpS5-MmpL5 trimeric complex
 RIGID BODY FIT REAL emd_53941_msk_1.map emd_53941_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 382.0 382.0 382.0 90.0 90.0 90.0 X Y Z -0.19120069 0.32627052 0.00020318087 0.007963087 0.955 0.955 0.955 AUTHOR Sharpened (Cryosparc) cryo-EM map of M.tuberculosis MmpS5L5-acpM complex. emd_53941_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 382.0 382.0 382.0 90.0 90.0 90.0 X Y Z -0.2140901 0.29330388 0.00020797884 0.02155165 0.955 0.955 0.955 AUTHOR Half map B emd_53941_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 382.0 382.0 382.0 90.0 90.0 90.0 X Y Z -0.261782 0.2903766 0.00021288115 0.021905432 0.955 0.955 0.955 AUTHOR Half map A