Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer)

2026-10-07 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-11-19 2026-10-07 2026-10-07 2026-10-07 Howard Hughes Medical Institute (HHMI) United States Cryo-EM structure of Leishmania tarentolae respiratory complex IV (cytochrome c oxidase dimer) Liao YT Chao L Electron transport chain, respiratory complex, cytochrome c oxidase, mitochondria, ELECTRON TRANSPORT Solayman M Liao YT Calvo SE Vacas AF Papanastasiou M Rivera KD Mani D Boyle BW Deng FG Betsinger CN Carr SA Chen MZ Duraisingh MT Fry MY Goyal M Issa TM Kim M Lian CG Luce BE Mian SY Nguyen K Paul AS Samuelson J Stefely JA Udeshi ND Mootha VK Aphasizheva I Chao LH Aphasizhev R Conserved and divergent mitochondrial assemblies in kinetoplastid parasites Mol.Cell US 86 4043 2026 doi:10.1016/j.molcel.2026.08.031 1097-2765 2168 MOCEFL 9zak FULLOVERLAP EMDB EMD-73966 associated EM volume

Leishmania tarentolae mitochondria Complex IV Leishmania tarentolae mitochondria Complex IV 0 16 9 5 2 8 17 15 4 11 7 10 1 6 14 12 13 3

Mitochondria were isolated from L. tarentolae promastigotes (UC strain). The mitochondrial pellet was resuspended and solubilized in lysis buffer, and then was incubated on ice for 10 min, followed by centrifuging at 14,000 x g for 10 min. The supernatant was filtered prior to grid preparation.

Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) P27 protein Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.025912837999999997 2 LEVO MSRCTTKISGGMARANLVDHGVYVKPMSLNPFLGAVHDGTSTGYCQGYSAKPMHWLYRFRYNLLPQGISGGFFSRNPYGR YVHWLEVSTIEKLRVQLLSLEAMPVSVLTTIVIIYTLWFSYRLAFLHPDITLYNLGLWSTKPWVQQQRFNKKIDIDQQVY RWVHRVPEFAITDPIREMYRLEISANEPYLEHVRDLGREKELTLYANERTGGAGNIRPLNIPH A0A640KL16 Cytochrome c oxidase subunit V, putative Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.020361263999999997 2 LEVO FFGKGWDNAALDTIFSSMLRKPEVNDRIRTQYASTMDPRDADVLRRLGEVSKENKTFIRVFLPPHLGDPHRLLKCYSLMA YPILDDKGGQLKVEMDGCKLDAFADPDDDYSKVVIPHIELVEYLAKSLLETMKWEATPRGAASLLESLYRGAEIPDHVFQ TPAVIERLEDYKDGNKVIS A0A640KIZ0 Cytochrome c oxidase subunit 2 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.023988639 2 LEVO MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLGLLLRLCL LLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIYKLWLSAVDVIHSFA ISSLGVKVDCIPGRCNEIVLFSSNNATVYGQCSELCGVLHGFMPIVICFI P14545 7.1.1.9 Cytochrome C oxidase subunit VI, putative Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.019310088 2 LEVO MPHEDHRKYKVQREELPRMPHFNDFNDPRFCGTTNKQKNGILAYYQWLHCIGNWGEEHSMCKKMRWYVERMMHETWLEKW EEKRALGHFDHTILYGVKPWKEFEPLYQPVKKNRKGAYEYWLDRDFEPLYDADAADWREKAPILHDMFVLGKKPVAE A0A640KLX8 Hypothetical protein, conserved, LtaP04.0630 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.023408184 2 LEVO MTMNFGNMTLGGAMATFGGQSNPMCNYTSPLAKKFVYKEVGKVHYPLRRHVFRTKVRTAAEIRFNEIVKRYMKEKMTFKR GCYAATITNTVELDHMGSIIPKDEYEVKRLTSYMTSKKMSSDYKKHMQELWTRVLFVCESTNLVGVTENAMHQNSRPGTD EEFMSIIWYSSFVTTLMAFVVTLFIWWYRYGQAPQYAEFK A0A640K7Y4 Cytochrome c oxidase VIII, putative Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.015495812999999999 2 LEVO MHSSDRFKAAWDEIPLHMLGASHKQMFEWYWRAMYQLGLRDPYRLTKLRSMLNWAALFSFMYLTYISIFYSSFYHVYMMD WPEHFKRENAREYALSHGHDVWAGDGKFIRPYFHINPPMLTMTSEDI A0A640KN71 Hypothetical protein, conserved, LtaP09.0030 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.012414288 2 LEVO MASCRTGRLPMPDDPLFNSTHMHGLRHSSRIAGLGMIAVIWIMYEKLRHSHHYITYKGPENPFARIRHRRFPGGAFMFGW GNNGLNRDCGIKEFECWAGYTGKEYTY A0A640K9E6 Cytochrome c oxidase VII, putative Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.019136926 2 LEVO MPRPFGVWAPATTLAEYRARIPNPFAYSFKWVYSMKREVFYPPEALAHFKDPQQFKDAVDTVIAMRVSDKIFGEGQKLPR HPVILMLMVLATHGFIIFSGLKYYYGTYMPANNPTWRKTVNKEWEEAINNSPWDHMSHVWQYSDEYAAALGDTAAPGQRK FYIPA A0A640KP32 Cytochrome-c oxidase Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.023705305 2 LEVO GPTPYQDKSYPVQPHNLDELQQPPDSWRKSPIMSKLMDQSLPVYDDVVTGVGRLYWQEPARVWHLFEADDTLMLEEHDRE EWNDRPYVAVNHLYEPPIGSEERPIRVEGTGNPGDQQIVLCFGNCAPHVPQSNYYMMMKGYNKTKCPMCQQWFYIHNRPW LVMHPDWTDEPAADEGPAYTFSEIEAEFDRDFHEFGVYLNAE A0A640KV26 Cytochrome c oxidase subunit 10 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.011616062 2 LEVO HFPLSPPPIEIDYLDSDPLEFAVRTEARRWGFDDLQYMRELAFVRIKENPSIGDFRRMTPEERRDLFWGSDRQDFFRYIT LKLTGHPEHLYHRGW A0A640KG51 Cytochrome c oxidase subunit I Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.012034609 2 LEVO YMLAFNSKAKARPNFGLRGVGYWTSEVYHKPGQNYWMVVCCAGPFLLVGAIMMDGFWSKLDDIAGGGPSALDYGWRSQDR KPWDFSFDIGEGYAAGPAVYRPASGAVDLG A0A640KXE6 Cytochrome c oxidase subunit 1 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.063297883 2 LEVO MFWLCLVCLSVSHKMIGLCYLLVAILSGFVGYVYSLFIRLELSLIGCGILFGDYQFYNVLITSHGLIMVFAFIMPVMMGG LVNYFIPVMAGFPDMVFPRLNNMSFWMYLAGFGCVVNGFLTEEGMGVGWTLYPTLICIDFHSSLACDFVMFAVHLLGISS ILNSINLLGTLFCCRRKFFSFLSWSLFIWAALITAILLIITLPVLAGGVTLILCDRNFNTSFYDVVGGGDLILFQHIFWF FGHPEVYIILLPVFGLISTIVEVIGFRCVFSTVAMIYSMILIAILGMFVWAHHMFVVGMDVDSRAYFGGVSILIGLPTCV KLFNWIYSFLYTDMIITFEVYFVIMFIFMFLIGAVTGLFLSNVGIDIMLHDTYFVVGHFHYVLSLGAVVGFFTGFIHFLA KWLPIELYLFWMFYFISTLFIGSNMLFFPMHSLGMYAFPRRISDYPVSFLFWSSFMLYGMLLLASLILFLCALFCVFLFW DYCLFFVSLFVFSLYCFFYFSTWLPCVMVLYLLLVDFAHIVLDYLFLILCFCFVFFIFFWQSLFLFFYI P14544 7.1.1.9 Cytochrome c oxidase subunit 3 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.034184578 2 LEVO MFVRVIFVGVSGVFVFLSLPAICIVYLTFCLCGLFCIMFGSFIFIDYCFICFFACLLFCLVCLLCDLFVDSLRGLFDVCC FIRCIQYCFVWFIISELLLFLSLFYVVFSLVLFVSVEFAFVFVIPVMFSCLICDFGFVFYWYFIDIFNLLINTFLLFVSG LFVNFVLFLFWFRFFLCVLFMLWVGILFGFLFLWNQVWEFALLFVTCSCGVFGSILFLIDLLHFSHVFLGIFLLFLCFSR CFNFLCMDTRFVFLYVVCLYWHFVDCVWFFLLRFVYFDVLSVVYLYA Q34935 Hypothetical protein, conserved, LtaP33.2260 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.010566061 2 LEVO FYANCGETGISGATMQVLLKLTLACCVVQVFAIRYFVFQRLTTKKQFVEDSTDLWESDGTEMDGEEAVANLRIQHERIMP FMNDIKDKLDAQA A0A640KQD4 Hypothetical protein, conserved, LtaP36.1760 Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.00970411 2 LEVO SYTELSHMKFPVYYGAVGVVLGYFVVMWVVFLRMGSKHTARSEFKNDYLRVWRRRLGTGYEWADAWGPEMGTFFKDLPEE VE A0A640KUH3 Cytochrome c oxidase subunit iv Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.035969211 2 LEVO HDRWYGHALELDTHNYKFNGEPPSWMKTHAKTEEETSFAKSVLPHIDFASSYECLLFDADRLNTNLNRKEFGNEIKYRLE KQANTVARAQQLLKDKKAGTGPDAAKIENTLIARIFDEEHVQAEMKYVKCIRANELAEDNRLDILPGGSPNSLREKTRWN LNTELHPADRAEIGARLTAWLPEKYHIVYFDDFQTVAANDATARREMLEIVESVQKEYTAEAKEGGYESDLKETVAELMD DVDPTRAITMEAIKSCKDLQQLEDWSRQVHEYNGDDRIIEIYARAAEITKNAEHQALVKQMREWRKLATKN A0A640KB61 Cytochrome c oxidase assembly factor like protein Leishmania tarentolae Leishmania tarentolae promastigotes (UC strain) 0.015137333 2 LEVO TVAKISSIERASTYLRFSTLRVHPHHEPNFRARPVGWKAWNSKQYMDPWAPYPLTSPVRHVDRPFSGMWFGMGHFALKNF FGPLNWKFWARVSFFGTLGWAYSLSSYALRMHRNGWEWKNRGAVFSMD A0A640K8B8 COPPER (II) ION 6.354599999999999e-05 2 CU HEME-A 0.000852837 4 HEA singleParticle particle 7.9

50 mM HEPES pH 7.9, 300 mM NaCl, 4 mM MgCl2, 20 uM CaCl2, 0.1 mM Dithiothreitol, and 0.5% n-dodecyl-beta-D-maltoside

Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE 90 ETHANE 100 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM OTHER FIELD EMISSION GUN 300 0.6 1.8 165000.0 FEI TITAN KRIOS AUTOGRID HOLDER GATAN K3 (6k x 4k) 52.0 1 cryoSPARC 4.7 PHASE FLIPPING AND AMPLITUDE CORRECTION C2 3.21 FSC 0.143 CUT-OFF cryoSPARC 4.7 5392 NOT APPLICABLE MAXIMUM LIKELIHOOD cryoSPARC 4.7 emd_73966.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 471.04 471.04 471.04 90.0 90.0 90.0 X Y Z -0.13428007 0.28947794 0.0004963049 0.010952361 0.736 0.736 0.736 0.0728 AUTHOR ::::EMDATABANK.org::::EMD-73966:::: Other in silico model

Built de novo using ModelAngelo (v1.014), guided by the cryo-EM density map

emd_73966_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 471.04 471.04 471.04 90.0 90.0 90.0 X Y Z -0.16522592 0.32727793 0.0004963049 0.0129872365 0.736 0.736 0.736 AUTHOR ::::EMDATABANK.org::::EMD-73966:::: sharp.map emd_73966_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 471.04 471.04 471.04 90.0 90.0 90.0 X Y Z -1.4740274 1.4939555 0.00042026222 0.18783443 0.736 0.736 0.736 AUTHOR ::::EMDATABANK.org::::EMD-73966:::: emd_73966_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 640 640 640 0 0 0 640 640 640 471.04 471.04 471.04 90.0 90.0 90.0 X Y Z -1.7111208 1.4944575 0.00042483612 0.18728907 0.736 0.736 0.736 AUTHOR ::::EMDATABANK.org::::EMD-73966::::