Plant Mitochondrial complex SC III2+IV from Vigna radiata composite map

2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY STRUCTURE_SUMMARY em_admin entity _em_admin.last_update _entity.formula_weight STRUCTURE_SUMMARY chem_comp chem_comp_atom chem_comp_bond database_2 em_3d_fitting_list em_admin entity pdbx_entity_nonpoly pdbx_entry_details pdbx_initial_refinement_model pdbx_modification_feature pdbx_validate_chiral _chem_comp.name _chem_comp.pdbx_synonyms _database_2.pdbx_DOI _database_2.pdbx_database_accession _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 _entity.pdbx_description _pdbx_entity_nonpoly.name _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_struct_conn_angle pdbx_validate_chiral struct_conn _chem_comp.formula _chem_comp.formula_weight _em_admin.last_update _entity.formula_weight RCSB RCSB 2020-08-12 2021-01-20 2021-01-20 2026-08-12 Plant Mitochondrial complex SC III2+IV from Vigna radiata composite map Maldonado M Letts JA mitochondria, respiration, bioenergetics, plants, OXIDOREDUCTASE Maldonado M Guo F Letts JA Atomic structures of respiratory complex III 2 , complex IV, and supercomplex III 2 -IV from vascular plants. Elife US 10 2021 33463523 doi:10.7554/eLife.62047 2050-084X 7jrp FULLOVERLAP PDB 7JRG unspecified

related structure from same publication

PDB 7JRO unspecified

related structure from same publication

EMDB EMD-22448 associated EM volume

Plant Mitochondrial complex SC III2+IV from Vigna radiata

Mitochondrial Respiratory Complex III2 Mitochondrial Respiratory Complex III2 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Vigna radiata hypocotyl mitochondria 0.485 Mitochondrial-processing peptidase subunit beta, mitochondrial isoform X1 Vigna radiata var. radiata 0.05871123799999999 2 LEVO MSLNRLLSAARRSDRRASALSSFRSLSASPALAPSAASPPAPPPPTAMIYDRAAEAIKSKLRQLENPDPRFLKHGNPRPA LSDHTRILAAPETRVTTLPNGLRVATESSLAARTATVGVWIDAGSRFETEETNGTAHFLEHMIFKGTERRNARELEEEIE NMGGHLNAYTSREQTTYYAKVTDSDVPQALDILADILQNSRFEENRISRERDVILREMEEVEGQTEEVIFDHLHATAFQY TPLGRTILGPAQNIKTITKAHLQSYIQTHYTAPRMVIAASGAVKHEDIVEQVKKLFTKLSTDATTTAQLVAKEPAIFTGS EVRMLDDDIPLAQFAVAFEGASWKDPDSIALMVMQAMLGSWNKTAGGGKHMGSELAQRVGINEVAESIMAFNTNYKDTGL FGVYAVAKPDCLDDLSYAIMQETTKLVYRVSEDDVTRACNQLKSSLLLHIDGTSPVAEDIGRQLLTYGRRIPFAELFARI DAVDASTIKRVANRFIYDKDVAIAAMGPIQRLPDYNWFRRRTYWNRY A0A1S3TWG4 Alpha-MPP Vigna radiata var. radiata 0.054537683999999996 2 LEVO MYRAAASSFRRHLKGHGSKLGSTRSSTSAAVAARTSKGGLFSWLTGERSSSLPSLDIPLGGVVLPDPLPDSVEQSKTKIT TLSNGLKIASETSPNPAASIGLYLDCGSIYETPFSSGASHLLERMAFKSTTNRSHFRIVREVEAIGGNIGASASREQMGY TFDALKTYVPQMVELLVDCVRNPAFLDWEVNEELRKVKAELGELSNNPQGLLLEAIHSAGYSGALAYPLLAPEAALNRLD GPSLEEFVAENYTAPRMVLAAAGVEHEELVSIAEPLLSDLPNVPRPDEPKSVYVGGDFRRHGESGGTHVALAFEVPGGWH KEKDAIVLTVLQMLMGGGGSFSAGGPGKGMHSRLYLRVLNEYQQIQSFSAFNSIFNNTGLFGIYASTSPDFAPKAVDIAA KELIAIASPGQVTQVQLDRAKKSTKSAVLMNLESRMIASEDIGRQILTYGERKPLEQFLKAVDEITLNDITKISQKIISS PLTMASYGDVLSVPSYESVNRKFHAK A0A1S3VF71 COB Vigna radiata 0.044353542999999995 2 LEVO MTIRNQRFSLLKEPISSTLNQHLIDYPTPSNLSYWWGFGSLAGICLVIQIVTGVFLAMHYTPHVDLAFNSVEHVMRDVEG GWLLRYMHANGASMFFIVVYLHIFRGLYYASYSSPREFVWCLGVVIFLLMIVTAFTGYVLPWGQMSFWGATVITSLASAI PVVGDTIVTWLWGGFSVDNATLNRFFSLHYLLPFLLVGASLLHLAALHQYGSNNPLGVHSEMDQISFYPYFYVKDLVGWV AFAIFFSIWIFYAPNVLGHPDNYIPANPMSTPPHIVPEWYFLPIYAILRSIPDKSGGVAAIALVFICLLALPFFKSMYVR SSSFRPIYQGIFWLLLADCLLLGWIGCQPVEAPFVTIGQISSFVFFLFFAITPILGRVGRGIPNSYTTDETEM cytochrome c1-2, heme protein, mitochondrial Vigna radiata var. radiata 0.033556188 2 LEVO MTGGVFQLLRRKLHPQFTNSSLLSPIIAKKDGAGSTGSRSLKVLALIGAGVSGFFSFSTVAVADEAEHGLACPSYPWPHK GILSSYDHASIRRGHQVYTEVCASCHSMSLISYRDLVGVAYTEEEVKAMAAEIEVVDGPNDEGEMFTRPGKLSDRFPQPY ANEAAARFANGGAYPPDLSLITKARHNGQNYVFSLLTGYRDPPAGVSIREGLHYNPYFPGGAIAMPKMLNDGAVEYEDGT PATEAQMGKDVVSFLSWAAEPEMEERKLMGFKWIFVLSLALLQAAYYRRLRWSVLKSRKLVLDVVN A0A1S3W199 Cytochrome b-c1 complex subunit Rieske, mitochondrial Vigna radiata var. radiata 0.030051432 2 LEVO MLRVAAKRLSSLSSSAWRANHAASAVLSRNPVAPSLSTEEHRSDPFSLRPEFFLPIRGYATDSLFHPKENSLIPEIPATV AAVKNPSSKIIYDEHNHERFPPGDPSKRAFAYFVLTGGRFVYASLIRLLVLKFVLSMSASKDVLALASLEVDLSSIEPGT TVTVKWRGKPVFIRRRTEDDIKLANSVDVASLRDPQQDAERVKNPEWLIVIGVCTHLGCIPLPNAGDFGGWFCPCHGSHY DISGRIRKGPAPYNLEVPTYTFLEENKLMIG A0A1S3TB49 7.1.1.8 Cytochrome b-c1 complex subunit 7 Vigna radiata var. radiata 0.014392697999999999 2 LEVO MASFLQSFLDPKKNWLAAQHMKSLVKRLSKYGLRYDDLYDPYYDLDVKEALNRLPKEVVDARHARLKRAIDLSMKHEYLP EDLQAMQTPFRGYLQDMLALVKRERAEREALGGLPLYQRSIP A0A1S3U9J1 cytochrome b-c1 complex subunit 8 Vigna radiata var. radiata 0.008349831 2 LEVO MGKQIVPVKSVIYALSPFQQKVMTGLWKDLPTKIHHKVSENWISATLLLGPLVGTYAYVQNYLEKEKLHHRY A0A1S3U9S5 Cytochrome b-c1 complex subunit 6 Vigna radiata var. radiata 0.008117424 2 LEVO MADEEPVDQKRYLEESCKPKCVKPLLEYQACIKRIHGDDSGQKHCTGQYFDYWFCVDKCVAPKLFTKLK A0A1S3VHC0 cytochrome b-c1 complex subunit 9 Vigna radiata var. radiata 0.00820342 2 LEVO METVARRRGGGIFESLYKVVMRRNSVYVTFVIAGAFLGERAVDYGIHKLWEANNVGKRYEDIPVLGQKLSEE A0A1S3TQD2 QCR10 Vigna radiata 0.008948875 2 LEVO MAGLPARLRIQPADVKAAAMWGVAAATGGLYLVQVSILVLPPVKVVFHFYLVSGFRICLDVKDLRTMPCSAPRIWRLYIL I COX1 Vigna radiata 0.057960559 1 LEVO MTNPVRWLFSTNHKDIGTLYFIFGAIAGVMGTCFSVLIRMELARPGDQILGGNHQLYNVLITAHAFLMIFFMVMPAMIGG FGNWFVPILIGAPDMAFPRLNNISFWLLPPSLLLLLSSALVEVGSGTGWTVYPPLSGITSHSGGAVDLAIFSLHLSGVSS ILGSINFITTIFNMRGPGMTMHRSPLFVWSVLVTAFLLLLSLPVLAGAITMLLTDRNFNTTFFDPAGGGDPILYQHLFWF FGHPEVYILILPGFGIISHIVSTFSGKPVFGYLGMVYAMISIGVLGFLVWAHHMFTVGLDVDTRAYFTAATMIIAVPTGI KIFSWIATMWGGSIQYKTPMLFAVGFIFLFTIGGLTGIVLANSGLDIALHDTYYVVAHFHYVLSMGAVFALFAGFYYWVG KIFGRTYPETLGQIHFWITFFGVNLTFFPMHFLGLSGMPRRIPDYPDAYAGWNALSSFGSYISVVGICCFFVVVTITSTS GNNITRANIPWAVEQNSTTLEWLVQSPPAFHTFGELPAIKETKSYVK Cytochrome c oxidase subunit 2 Vigna radiata var. radiata 0.028391602 1 LEVO MCGGFPAISFCDAPEPWQLGFQDAATPIMQGIMDLHHDIFFFLVQIAVFVLWVLSRALWCFRSKISPIPQRIVHGTTIEI LWTIFPSIILMFIAIPSFTLLYSMDDVVVDPAITIKAIGHQWYWSYEYSDYNNSDEQSLAFDSYMVPEDDLELGQLRLLE VDNRVVVPAKTHLRVLITSADVLHSWAVPSLGVKCDAVPGRLNQISTFIQREGVYYGQCSEICGTNHAFMPIVVEAVSTK DYGSWVSNQIQ A0A1S3TZB2 COX3 Vigna radiata 0.029967893 1 LEVO MIESQRHSYHLVDPSPWPISGSLGALATTVGGVMYMHSFQGGATLLSLGLIFILYTMFVWWRDVLRESTLEGHHTKVVQL GLRYGFILFIVSEVMFLFAFFWAFFHSSLAPTVEIGGIWPPLGIWVLDPWEIPFLNTLILLSSGAAVTWAHHAILAGKEK RAVYALVATVLLALVFTGFQGMEYYQAPFTISDSIYGSTFFLATGFHGFHVIIGTLFLIICGIRQYLGHLTKEHHVGFEA AAWYWHFVDVVWLFLFVSIYWWGGI COX4 Vigna radiata var. radiata 0.00881102 1 LEVO MSTKYIVSAILGSFGIAWVCDYYVSEKKIFGGSTPGTITNKEWGEETDKKFQAWPRTAGPPVVVNPITRQNFVVKSRSE A0A1S3TNX9 cytochrome c oxidase subunit 5b-2, mitochondrial Vigna radiata var. radiata 0.016694705 1 LEVO MLRRFLSHSNLRSLHTALSPSRPRFAAPLLTRHVTAQSGASSVRKRVEDVVPIATGHEREEIQASLEGRDILEINHPEGP FGTKEAPAIVKSYFDRRIVGCPGGEGEDEHDVVWFWLENGKPHECPVCSQYFELKVVGPGGDPYGHGDHH A0A1S3U1E4 cytochrome c oxidase subunit 6a, mitochondrial Vigna radiata var. radiata 0.011225671 1 LEVO MATSLVRSGFLRTALRGGARGSQVPKRNFSSAGHHDDAYETAKWEKITYLGIVSCTGLAIYNLSKGHPHTEEPPAYPYLH IRNKEFPWGPDGLFETKKHH A0A1S3UMA0 cytochrome c oxidase subunit 6b-1 Vigna radiata var. radiata 0.020018634999999996 1 LEVO MAETAANKSQSLAEEYHVSDKQEKTAVVEKPVEVKEVENPQEAGSVEAVVEKIVEETTPVAPAVAQESSEVSPPPAEESA EESTEEQSSGNVEDNSGNEDAAEKTPEIKLETAPADFRFPTTNQTRHCFTRYIEYHRCVAAKGEGASECDKFAKYYRSLC PGEWIDRWNEQRENGTFPGPL A0A1S3VV60 Cytochrome c oxidase subunit 5C Vigna radiata var. radiata 0.007120326 1 LEVO MAGPRIAHATLKGPSVVKEIIIGITLGLAAGSVWKMHHWNEQRKIRTFYDLLEKGEIGVVVDEQ A0A1S3V319 COX7a Vigna radiata var. radiata 0.0076229309999999995 1 LEVO MSEPPFRPREKLIEKQKHFQSVHKHTYLKGPYDKITSVAIPLALAASSLYLIGRGIYNMSHGIGKKE A0A1S3TUX2 COX7c Vigna radiata var. radiata 0.010505157999999999 1 LEVO MAFNNALRSAAKLIASSESSISTSVSRGFHSTPMKRMGGGHGHDEPYYIHAKHMYNLDRMKHRGLKMSLAVFSAFSIGVA VPVYAVIFQQKKTASA A0A1S3V7C2 ZINC ION 6.5409e-05 3 ZN 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 5 PC1 CARDIOLIPIN 0.0014640429999999997 9 CDL PROTOPORPHYRIN IX CONTAINING FE 0.000616487 4 HEM 1,2-Distearoyl-sn-glycerophosphoethanolamine 0.000748065 29 3PE HEME C 0.0006205189999999999 2 HEC HEME-A 0.000852837 2 HEA COPPER (II) ION 6.354599999999999e-05 1 CU MAGNESIUM ION 2.4305e-05 1 MG DINUCLEAR COPPER ION 0.00012709199999999998 1 CUA LYSINE 0.00014719499999999998 1 LYS singleParticle particle 6 7.8 20.0 HEPES 150.0 NaCl sodium chloride 1.0 EDTA 0.2 digitonin Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 30 AIR ETHANE 100 288 FEI VITROBOT MARK III

This sample was monodisperse on size exclusion chromatography but was a mixture of different mitochondrial respiratory complexes

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.5 3.0 60010.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 5760 4092 1 9816 3.0 86.4 1 150000000 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio model generation

C1 3.8 FSC 0.143 CUT-OFF RELION 29348 OTHER cryoSPARC

Stochastic gradient descent

OTHER cryoSPARC

Stochastic gradient descent

emd_22448.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 426.5984 426.5984 426.5984 90.0 90.0 90.0 Z Y X -36.912239999999997 45.661976000000003 0.00015192044 1.1589029 0.8332 0.8332 0.8332 6.0 AUTHOR ::::EMDATABANK.org::::EMD-22448:::: Plant mitochondrial supercomplex III2 IV from Vigna radiata. Composite map. 6Q9E PDB experimental model 6HU9 PDB experimental model AB INITIO MODEL correlation coefficient REAL 67.0