2025-10-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY database_2 em_admin _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_unobs_or_zero_occ_atoms pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update PDBe PDBe 2020-04-10 2020-09-09 2020-09-09 2025-10-01 Swedish Research Council 2014-4116 Sweden Swedish Research Council 2018-03694 Sweden Knut and Alice Wallenberg Foundation 2017.0091 Sweden Knut and Alice Wallenberg Foundation 2013.0006 Sweden CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae Berndtsson J Rathore S Ott M Complex, CIII, CIV, Supercomplex, ELECTRON TRANSPORT Berndtsson J Aufschnaiter A Rathore S Marin-Buera L Dawitz H Diessl J Kohler V Barrientos A Buttner S Fontanesi F Ott M Respiratory supercomplexes enhance electron transport by decreasing cytochrome c diffusion distance. Embo Rep. UK 21 e51015 e51015 2020 33016568 doi:10.15252/embr.202051015 1469-3178 6ymx FULLOVERLAP PDB 6GIQ re-refinement
This work is a re-refinement of the data of 6GIQ, with a new density map, and a new model
 EMDB EMD-10847 associated EM volume
CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae
 Respiratroy supercopmlex CIII2/CIV Respiratroy supercopmlex CIII2/CIV 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) W303-1b Mitochondria Cytochrome c oxidase subunit 1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.058316938 1 LEVO WLYSTNAKDIAVLYFMLAIFSGMAGTAMSLIIRLELAAPGSQYLHGNSQLFNVLVVGHAVLMIFFLVMPALIGGFGNYLL PLMIGATDTAFPRINNIAFWVLPMGLVCLVTSTLVESGAGTGWTVYPPLSSIQAHSGPSVDLAIFALHLTSISSLLGAIN FIVTTLNMRTNGMTMHKLPLFVWSIFITAFLLLLSLPVLSAGITMLLLDRNFNTSFFEVSGGGDPILYEHLFWFFGHPEV YILIIPGFGIISHVVSTYSKKPVFGEISMVYAMASIGLLGFLVWSHHMYIVGLDADTRAYFTSATMIIAIPTGIKIFSWL ATIHGGSIRLATPMLYAIAFLFLFTMGGLTGVALANASLDVAFHDTYYVVGHFHYVLSMGAIFSLFAGYYYWSPQILGLN YNEKLAQIQFWLIFIGANVIFFPMHFLGINGMPRRIPDYPDAFAGWNYVASIGSFIATLSLFLFIYILYDQLVNGLNNKV NNKSVIYNKAPDFVESNTIFNLNTVKSSSIEFLLTSPPAVHSFNTPAVQS P00401 1.9.3.1 Cytochrome c oxidase subunit 2 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.026779815999999998 1 LEVO DVPTPYACYFQDSATPNQEGILELHDNIMFYLLVILGLVSWMLYTIVMTYSKNPIAYKYIKHGQTIEVIWTIFPAVILLI IAFPSFILLYLCDEVISPAMTIKAIGYQWYWKYEYSDFINDSGETVEFESYVIPDELLEEGQLRLLDTDTSMVVPVDTHI RFVVTAADVIHDFAIPSLGIKVDATPGRLNQVSALIQREGVFYGACSELCGTGHANMPIKIEAVSLPKFLEWLNEQ P00410 1.9.3.1 Cytochrome c oxidase subunit 3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.030252390999999997 1 LEVO THLERSRHQQHPFHMVMPSPWPIVVSFALLSLALSTALTMHGYIGNMNMVYLALFVLLTSSILWFRDIVAEATYLGDHTM AVRKGINLGFLMFVLSEVLIFAGLFWAYFHSAMSPDVTLGACWPPVGIEAVQPTELPLLNTIILLSSGATVTYSHHALIA GNRNKALSGLLITFWLIVIFVTCQYIEYTNAAFTISDGVYGSVFYAGTGLHFLHMVMLAAMLGVNYWRMRNYHLTAGHHV GYETTIIYTHVLDVIWLFLYVVFYWWGV P00420 1.9.3.1 Cytochrome c oxidase subunit 4, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.012694381999999999 1 LEVO VVKTAQNLAEVNGPETLIGPGAKEGTVPTDLDQETGLARLELLGKLEGIDVFDTKPLDSSRKGTMKDPIIIESYDDYRYV GCTGSPAGSHTIMWLKPTVNEVARCWECGSVYKLNPV P04037 Cytochrome c oxidase subunit 5A, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.014324147 1 LEVO ALSNAAVMDLQSRWENMPSTEQQDIVSKLSERQKLPWAQLTEPEKQAVWYISYGEWGPRRPVLNKGDSSFIAKGVAAGLL FSVGLFAVVRMAGGQDAKTMNKEWQLKSDEYLKSKNANPWGGYSQVQS P00424 Cytochrome c oxidase subunit 6, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.011725173 1 LEVO ETFEEFTARYEKEFDEAYDLFEVQRVLNNCFSYDLVPAPAVIEKALRAARRVNDLPTAIRVFEALKYKVENEDQYKAYLD ELKDVRQELGVPLKEELFP P00427 Cytochrome c oxidase subunit 7, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.006410639 1 LEVO NKVIQLQKIFQSSTKPLWWRHPRSALYLYPFYAIFAVAVVTPLLYIPNAIRGIKA P10174 Cytochrome c oxidase subunit 8, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.005737734999999999 1 LEVO VHFKDGVYENIPFKVKGRKTPYALSHFGFFAIGFAVPFVACYVQLKKSGAF P04039 Cytochrome c oxidase subunit 9, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.006241401 1 LEVO IAPITGTIKRRVIMDIVLGFSLGGVMASYWWWGFHMDKINKREKFYAELAERK P07255 Cytochrome c oxidase subunit 12, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.009225290999999998 1 LEVO NSPLHTVGFDARFPQQNQTKHCWQSYVDYHKCVNMKGEDFAPCKVFWKTYNALCPLDWIEKWDDQREKGIFAGDINSD Q01519 Cytochrome c oxidase subunit 13, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.013306061 1 LEVO NALKPAFGPPDKVAAQKFKESLMATEKHAKDTSNMWVKISVWVALPAIALTAVNTYFVEKEHAEHREHLKHVPDSEWPRD YEFMNIRSKPFFWGDGDKTLFWNPVVNRHIEHDD P32799 Cytochrome c oxidase subunit 26, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.004347023 1 LEVO ESWVITEGRRLIPEIFQWSAVLSVCLGWPGAVYFFSKA Q2V2P9 Cytochrome b-c1 complex subunit 1, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.04745927 2 LEVO AEVTQLSNGIVVATEHNPSAHTASVGVVFGSGAANENPYNNGVSNLWKNIFLSKENSAVAAKEGLALSSNISRDFQSYIV SSLPGSTDKSLDFLNQSFIQQKANLLSSSNFEATKKSVLKQVQDFEENDHPNRVLEHLHSTAFQNTPLSLPTRGTLESLE NLVVADLESFANNHFLNSNAVVVGTGNIKHEDLVNSIESKNLSLQTGTKPVLKKKAAFLGSEVRLRDDTLPKAWISLAVE GEPVNSPNYFVAKLAAQIFGSYNAFEPASRLQGIKLLDNIQEYQLCDNFNHFSLSYKDSGLWGFSTATRNVTMIDDLIHF TLKQWNRLTISVTDTEVERAKSLLKLQLGQLYESGNPVNDANLLGAEVLIKGSKLSLGEAFKKIDAITVKDVKAWAGKRL WDQDIAIAGTGQIEGLLDYMRIRSDMSMMRW P07256 Cytochrome b-c1 complex subunit 2, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.038751917999999996 2 LEVO LTVSARDAPTKISTLAVKVHGGSRYATKDGVAHLLNRFNFQNTNTRSALKLVRESELLGGTFKSTLDREYITLKATFLKD DLPYYVNALADVLYKTAFKPHELTESVLPAARYDYAVAEQCPVKSAEDQLYAITFRKGLGNPLLYDGVERVSLQDIKDFA DKVYTKENLEVSGENVVEADLKRFVDESLLSTLPAGKSLVSKSEPKFFLGEENRVRFIGDSVAAIGIPVNKASLAQYEVL ANYLTSALSELSGLISSAKLDKFTDGGLFTLFVRDQDSAVVSSNIKKIVADLKKGKDLSPAINYTKLKNAVQNESVSSPI ELNFDAVKDFKLGKFNYVAVGDVSNLPYLDEL P07257 Cytochrome b Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.04368659 2 LEVO MAFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEHIMRDVHNGYILRY LHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGND IVSWLWGGFSVSNPTIQRFFALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLIL ALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAILVLLVLPFTDRSVVRGNTFKV LSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYFLIIVPVISTIENVLFYIGRVNK P00163 7.1.1.8 Cytochrome c1, heme protein, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.027807395 2 LEVO MTAAEHGLHAPAYAWSHNGPFETFDHASIRRGYQVYREVCAACHSLDRVAWRTLVGVSHTNEEVRNMAEEFEYDDEPDEQ GNPKKRPGKLSDYIPGPYPNEQAARAANQGALPPDLSLIVKARHGGCDYIFSLLTGYPDEPPAGVALPPGSNYNPYFPGG SIAMARVLFDDMVEYEDGTPATTSQMAKDVTTFLNWCAEPEHDERKRLGLKTVIILSSLYLLSIWVKKFKWAGIKTRKFV FNPPKPRK P07143 7.1.1.8 Cytochrome b-c1 complex subunit Rieske, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.020122955 2 LEVO KSTYRTPNFDDVLKENNDADKGRSYAYFMVGAMGLLSSAGAKSTVETFISSMTATADVLAMAKVEVNLAAIPLGKNVVVK WQGKPVFIRHRTPHEIQEANSVDMSALKDPQTDADRVKDPQWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGSHYDISGR IRKGPAPLNLEIPAYEFDGDKVIVG P08067 7.1.1.8 Cytochrome b-c1 complex subunit 6, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.008854791999999998 1 LEVO VTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHYLDTATAPRLFDKLK P00127 Cytochrome b-c1 complex subunit 7, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.014452557 2 LEVO PQSFTSIARIGDYILKSPVLSKLCVPVANQFINLAGYKKLGLKFDDLIAEENPIMQTALRRLPEDESYARAYRIIRAHQT ELTHHLLPRNEWIKAQEDVPYLLPYILEAEAAAKEKDELDNIEVSK P00128 Cytochrome b-c1 complex subunit 8, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.010856314 2 LEVO GPPSGKTYMGWWGHMGGPKQKGITSYAVSPYAQKPLQGIFHNAVFNSFRRFKSQFLYVLIPAGIYWYWWKNGNEYNEFLY SKAGREELERVNV P08525 Cytochrome b-c1 complex subunit 9, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.006214155 1 LEVO SLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIAA P22289 Cytochrome b-c1 complex subunit 6, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.008983905 1 LEVO EVTDQLEDLREHFKNTEEGKALVHHYEECAERVKIQQQQPGYADLEHKEDCVEEFFHLQHYLDTATAPRLFDKLK P00127 Cytochrome b-c1 complex subunit 9, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.006230154999999999 1 LEVO SSLYKTFFKRNAVFVGTIFAGAFVFQTVFDTAITSWYENHNKGKLWKDVKARIA P22289 Cytochrome b-c1 complex subunit 10, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.004920734 1 LEVO KTGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQD P37299 Cytochrome b-c1 complex subunit 10, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) 0.005750779 1 LEVO TGLHFGRLSLRSLTAYAPNLMLWGGASMLGLFVFTEGWPKFQDTLYKKIPL P37299 COPPER (II) ION 6.354599999999999e-05 1 CU HEME-A 0.000852837 2 HEA PHOSPHATIDYLETHANOLAMINE 0.0007340389999999999 7 PTY (2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate 0.0008348619999999999 2 CN3 DINUCLEAR COPPER ION 0.00012709199999999998 1 CUA 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE 0.0007340389999999999 5 PCF ZINC ION 6.5409e-05 1 ZN (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate 0.000592785 2 6PH PROTOPORPHYRIN IX CONTAINING FE 0.000616487 6 HEM (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate 0.0006919589999999999 2 8PE (5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate 0.000634631 1 CN5 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL 0.0005928909999999999 2 UQ6 (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate 0.000593773 2 9PE (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate 0.000564732 2 7PH FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES singleParticle particle 7.4 10.0 C4H11NO3 Tris 150.0 NaCl Sodium chloride 0.1 C56H92O29 Digitonin 1.0 C7H7FO2S phenylmethylsulfonyl fluoride Homemade COPPER 400 CARBON LACEY GLOW DISCHARGE AIR ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 -0.0014 -0.003 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 8775 9.0 40.0 1 647805 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION
ab initio
 1 C1 3.17 FSC 0.143 CUT-OFF cryoSPARC 2 201223 OTHER cryoSPARC 2
SGD
 MAXIMUM LIKELIHOOD cryoSPARC 2 cryoSPARC 2 emd_10847.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 370 370 370 0 0 0 370 370 370 392.2 392.2 392.2 90.0 90.0 90.0 X Y Z -1.2400135 2.3732495 0.0059492365 0.06867311 1.0600001 1.0600001 1.0600001 0.25 AUTHOR emd_10847_msk_1.map emd_10847_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 370 370 370 0 0 0 370 370 370 392.2 392.2 392.2 90.0 90.0 90.0 X Y Z -0.43764096 1.5644833 0.0044701006 0.067494154 1.0600001 1.0600001 1.0600001 AUTHOR First half map emd_10847_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 370 370 370 0 0 0 370 370 370 392.2 392.2 392.2 90.0 90.0 90.0 X Y Z -0.41623962 1.4909635 0.0044568316 0.06740879 1.0600001 1.0600001 1.0600001 AUTHOR Second half map