2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight DATABASE_REFERENCES citation em_admin pdbx_database_proc pdbx_seq_map_depositor_info _citation.journal_volume _citation.page_first _citation.page_last _em_admin.last_update _pdbx_seq_map_depositor_info.one_letter_code _pdbx_seq_map_depositor_info.one_letter_code_mod STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond em_admin entity pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_chiral _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight PDBe PDBe 2021-04-01 2021-10-13 2021-10-13 2026-09-02 H2020 Marie Curie Actions of the European Commission 754411 Austria Vercellino I Sazanov LA mitochondria, respiratory chain, supercomplex, OXIDOREDUCTASE, complex III, complex IV, MEMBRANE PROTEIN Vercellino I Sazanov LA Nature UK 598 364 367 2021 34616041 doi:10.1038/s41586-021-03927-z 1476-4687 0006 NATUAS 7o3h FULLOVERLAP PDB 7O37 unspecified

Full murine supercomplex CIII2CIV in the locked conformation

PDB 7O3C unspecified

Full murine supercomplex CIII2CIV in the unlocked conformation

PDB 7O3E unspecified

Intermediate murine supercomplex CIII2CIV in the locked conformation

EMDB EMD-12706 associated EM volume

Murine CIII2 focus-refined from supercomplex CICIII2

Murine complex CIII2 focus-refined from supercomplex CICIII2 Murine complex CIII2 focus-refined from supercomplex CICIII2 0 1 2 3 4 5 6 7 8 9 10 11

Dimer of Complex III

Mus musculus CD1 heart cardiac muscle mitochondria inner mitochondrial membrane 0.5 Cytochrome b-c1 complex subunit 1, mitochondrial Mus musculus heart 0.049355301 2 LEVO TATFAQALQSVPETQVSILDNGLRVASEQSSHATCTVGVWIDAGSRYETEKNNGAGYFLEHLAFKGTKNRPGNALEKEVE SIGAHLNAYSTREHTAYLIKALSKDLPKVVELLADIVQNSSLEDSQIEKERDVILREMQENDASMQNVVFDYLHATAFQG TPLAQAVEGPSENVRRLSRTDLTDYLNRHYKAPRMVLAAAGGVEHQQLLDLAQKHLSSVSRVYEEDAVPGLTPCRFTGSE IRHRDDALPLAHVAIAVEGPGWANPDNVTLQVANAIIGHYDCTYGGGVHLSSPLASVAVANKLCQSFQTFNISYSDTGLL GAHFVCDAMSIDDMVFFLQGQWMRLCTSATESEVTRGKNILRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIQ EVDAQMLRDICSKYFYDQCPAVAGYGPIEQLPDYNRIRSGMFWLRF Q9CZ13 Cytochrome b-c1 complex subunit 2, mitochondrial Mus musculus heart 0.046641773 2 LEVO SLKVAPKVKTSAAPGGVPLQPQDLEFTKLPNGLVIASLENYAPLSRIGLFVKAGSRYEDSNNLGTSHLLRLASSLTTKGA SSFKITRGIEAVGGKLSVTATRENMAYTVEGIRSDIEILMEFLLNVTTAPEFRRWEVAALRSQLKIDKAVAFQNSQTRII ENLHDVAYKNALANPLYCPDYRMGKITSEELHYFVQNHFTSARMALVGLGVSHSVLKQVAEQFLNMRGGLGLAGAKAKYR GGEIREQNGDNLVHAAIVAESAAIGNAEANAFSVLQHLLGAGPHIKRGNNTTSLLSQSVAKGSHQPFDVSAFNASYSDSG LFGIYTISQAAAAGEVINAAYNQVKAVAQGNLSSADVQAAKNKLKAGYLMSVETSEGFLSEIGSQALAAGSYMPPSTVLQ QIDSVADADVVKAAKKFVSGKKSMAASGNLGHTPFLDEL Q9DB77 Cytochrome b Mus musculus heart 0.043240305 2 LEVO MTNMRKTHPLFKIINHSFIDLPAPSNISSWWNFGSLLGVCLMVQIITGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIR YMHANGASMFFICLFLHVGRGLYYGSYTFMETWNIGVLLLFAVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTTL VEWIWGGFSVDKATLTRFFAFHFILPFIIAALAIVHLLFLHETGSNNPTGLNSDADKIPFHPYYTIKDILGILIMFLILM TLVLFFPDMLGDPDNYMPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALILSILILALMPFLHTSKQRSLMFRPI TQILYWILVANLLILTWIGGQPVEHPFIIIGQLASISYFSIILILMPISGIIEDKMLKLYP P00158 Cytochrome c1, heme protein, mitochondrial Mus musculus heart 0.027312187999999998 2 LEVO SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEEEAKALAEEVEVQDGPNDDGEM FMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRARHGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGM APPIYTEVLEYDDGTPATMSQVAKDVATFLRWASEPEHDHRKRMGLKMLLMMGLLLPLTYAMKRHKWSVLKSRKLAYRPP K Q9D0M3 7.1.1.8 Cytochrome b-c1 complex subunit Rieske, mitochondrial Mus musculus heart 0.021524398 2 LEVO SHTDVKVPDFSDYRRAEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVSSMSASADVLAMSKIEIKLSD IPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDPQHDLDRVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPC HGSHYDASGRIRKGPAPLNLEVPAYEFTSDDVVVVG Q9CR68 7.1.1.8 Cytochrome b-c1 complex subunit 7 Mus musculus heart 0.013456336 2 LEVO AGRSAVSASSKWLDGFRKWYYNAAGFNKLGLMRDDTLHETEDVKEAIRRLPEDLYNDRMFRIKRALDLTMRHQILPKDQW TKYEEDKFYLEPYLKEVIRERKEREEWAKK Q9CQB4 Cytochrome b-c1 complex subunit 8 Mus musculus heart 0.009652050999999998 2 LEVO GREFGNLARIRHVISYSLSPFEQRAFPSYFSKGIPNVLRRTRERILRVAPPFVVVYLIYTWGNQEFEQSKRKNPAMYEND K Q9CQ69 Cytochrome b-c1 complex subunit 6, mitochondrial Mus musculus heart 0.009002014999999999 2 LEVO GDPKEEEEEELVDPLTTVREHCEQLEKCVKARERLELCDNRVSSRSQTEEDCTEELFDFLHARDHCVAHKLFKNLK P99028 Cytochrome b-c1 complex subunit 9 Mus musculus heart 0.00732633 2 LEVO SSPTIPSRLYSLLFRRTSTFALTIAVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYENKE Q8R1I1 Cytochrome b-c1 complex subunit 10 Mus musculus heart 0.006546627 2 LEVO MLSRFLGPRYRELARNWIPTAGMWGTVGAVGLVWATDWRLILDWVPYINGKFKKDD Q9CPX8 Cytochrome b-c1 complex subunit 9 Mus musculus heart 0.007900234 1 LEVO MLSVAARSGPFAPVLSATSRGVAGALRPLLQGAVPAASEPPVLDVKRPFLCRESLSGQAAARPLVATVGLNVPASVRF Q9CR68 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 8 3PE CARDIOLIPIN 0.0014640429999999997 6 CDL PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM HEME C 0.0006205189999999999 2 HEC FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 2 PC1 singleParticle particle 4 7.7 20.0 C8H18N2O4S HEPES 200.0 NaCl sodium chloride 2.0 C10H16N2O8 EDTA 0.2 C32H58N2O7S CHAPS

CHAPS was added only upon freezing

Quantifoil R0.6/1 COPPER 300 CARBON CONTINUOUS 1.0 GLOW DISCHARGE 5 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.4 0.2 1.6 2.7 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 1 7245 1.17 90.66 1 1500000

multiple rounds of picking and classification performed, first with Relion LoG and then with Topaz, to extract the best particles from the non-pure starting material

Gctf used for per-particle defocus CTFFIND used for initial CTF estimation RELION 3.1 used for CTF refinement PHASE FLIPPING AND AMPLITUDE CORRECTION 6QBX

PDB 6qbx used for initial classification of CICIII2

1 C1 FOURIER SPACE 2.6 FSC 0.143 CUT-OFF RELION 3.1

the final pool of particles was classified without alignment around the MPP cavity to separate the two orientations of Sub 9. the two classes were then refined, first globally and then focused on CIII, re-oriented along the C2 symmetry axis, to allow for subsequent 180 degrees flipping of one class and final re-pooled refinement with all particles having the same orientation of Sub 9

129 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 5 116400.0 RELION 3.1

the particles were not evenly distributed in the classes. the good class contained 129k particles

1NTZ PDB experimental model 3L75 PDB experimental model OTHER MAXIMAL LIKELIHOOD REAL 65.0