2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update RCSB RCSB 2020-06-01 2020-09-02 2020-09-02 2026-08-12 Letts JA Maldonado M respiration, mitochondria, electron transport chain, complex I, MEMBRANE PROTEIN Maldonado M Padavannil A Zhou L Guo F Letts JA Elife US 9 2020 32840211 doi:10.7554/eLife.56664 2050-084X 6x89 FULLOVERLAP EMDB EMD-22090 associated EM volume

Vigna radiata mitochondrial complex I*

Vigna radiata complex I* Vigna radiata complex I* 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 26 27 28 29 30 31 32 33 34

Complex I 800 kDa assembly intermediate (complex I*)

Vigna radiata 0.8 Unknown Peptide Vigna radiata 0.001549902 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 Vigna radiata 0.010884631999999998 1 LEVO MAWRGQLSKNIKELRFLMCQSSSASASARAFVEKNYKELKTLNPKLPILIRECSGVEPQLWARYDLGVEKAIKLEGLSEA QISKALEDLAKAGQSSKA A0A1S3TVC7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial Vigna radiata 0.018977604 1 LEVO MFLRAVARPLMAKVKASTGIVGLEVVPNAREVLIGLYSKTLKEIQKVPEDEGYRKAVESFTKHRLSVCKEEEDWEAIEKR LGCGQVEELIEEAQDELKLISYMIEWDPWGVPDDYECEVIENDAPVPKHVPLHRPPPLPTEFHKTLEALSSQSGKDIPGA SSTESPSKT A0A1S3U023 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 Vigna radiata 0.014920033999999999 1 LEVO MASALRNVKVLPNSASVEEARQRVFDFFRATCRSLPSVMEIYNLYDVTSVAQLRSTVASEIRKNIGVSDPKVIDMLLFKG MEELMNVVNHSKQRHHIIGQYVVGQQGQVQDSASKDPAISPFLKNFYSSNYF A0A1S3W1K8 NDUA7 Vigna radiata 0.014356375999999999 1 LEVO MAKSASNSLVQTLKRYIKKPWEITGPCADPEYRSAVPLATEYRLQCPATTKEKPCIPNSLPETVYDIKYFSRDQRRNRPP IRRTVLKKADVEKLAKEQTFAVSDFPPVYLNSAVEEDINAIGGGYQG A0A1S3UVC7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial isoform X1 Vigna radiata 0.043781504 1 LEVO MQTIARRLGHQSLKSSTSIRAIYPISDHHYVADHQRYVSTIATKGVGHLVRKGTGGRSSVSGIIATVFGATGFLGRYVVQ QLAKMGSQVLVPFRGSEDCPRHLKLMGDLGQIVPMKYNPRDESSVKAVMAKANVVINLIGRDYETRNYSFEEVHYHMAEN LAKISREHGGILRFIQVSCLGASPSSPSRMLRAKAAAEEVVLRELPEATILKPAVMIGTEDRILNPWAHFAKKYGFIPLF GNGSTKIQPVYVVDVAAALTTVLKDDGTSMGKTYELGGPEIFTVHDLAELMYETIREWPRYVKVPFPIAKALATPREILL NKVPFPLPTPEILNLDKIQALTTDTIVSENALTFNDLGIIPHKLKGYPVEFLISYRKGGPQFGSTISERVTPDAWP A0A1S3V8W7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 Vigna radiata 0.018192482 1 LEVO MASVVKNVLKSIREKGFGTFLRELKDEGYLRCLPDGNLLQTKIHNIGATLVGVDKFGNKYYEKLGDTQYGRHRWVEYAEK SRYNASQVPPEWHGWLHFITDHTGDELLLLKPKRYGVEHKENLSGEGEQYIYHSKGHALNPGQRDWTRYQPWESKA A0A1S3VNK7 NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial Vigna radiata 0.08143421899999999 1 LEVO MGFGLLASKALRPTSRLLLSSQNPTIFLRTIVSKPQLCNPEASAAQPAQPPPVDLPPRSPLAGARVHFANPDDAIEVFVD GYPVKIPKGMTVLQACEVAGVDIPRFCYHSRLSIAGNCRMCLVEVEKSPKPVASCAMPALPGMKIKTDTPVAKKAREGVM EFLLMNHPLDCPICDQGGECDLQDQSMAFGSDRGRFTEVKRSVVDKNLGPLVKTVMTRCIQCTRCVRFATEVAGVQDLGM LGRGSGEEIGTYVEKLLTSELSGNVIDICPVGALTSKPFAFKARNWELKGTETIDVTDAVGSNIRIDSRGPEVMRIVPRL NEDINEEWISDKTRFCYDGLKRQRLNDPMIRGPDGRFKAVNWRDALSVIADIAHQVKPEEIVGVAGKLSDAESMIALKDF LNRMGSNDVWGEGIGVNTNADFRSGYIMNTSIAGLEKADVFLLVGTQPRVEAAMVNARIRKTVRSNQAKVGYIGPATDFN YDHKHLGTDPQTLVEIAEGRHPFFKTLSDAKNPVIIVGAGVFERKDQDAIFAAVETIAQKANVVRPDWNGLNVLLLHAAQ AAALDLGLVPQSEKSLESAKFVYLMGADDVNLDKIPDDAFVVYQGHHGDKSVYRANVILPTAAFSEKEGTYQNTEGCTQQ TLPAVPTVGDSRDDWKIIRALSEVAGVRLPYDTIGAVRARIRNVAPNLVNVDEREPATLPSSLRPSFTQKVDTTPFGTVI ENFYMTDAITRASKIMAQCSATLLKK A0A1S3TQ85 NDUS2 Vigna radiata 0.044813281 1 LEVO MTTRNGQIKNFTSNFGPQHPAAHGVLRSVLEMNGEVVERAEPHIGLLHRGTEKLIEYKTYLQALPYFDRLDYVSTMAQEH AYSLAVERLLNCEVPLRAQYIRVLFCEITRILNHLLALTTHAMDVGASTPSLWAFEEREKLLEFYERVSGARMHASFIRP GGVAQDLPLGLCRDIDSFTQQFASRIDELEEMLTGNRIWKQRLVDIGTVTAQQAKDWGFSGVMLRGPGVCWDLRRAAPYD VYDQLDFDVPVGTRGDCYDRYCIRIEEMRQSMRIIWQCPNKIPSGMIKADDRKLCPPSRCRMKLSMESSIHHFELYTEGF SVPAPSTYTAVEAPKGEFGVFLVSNGSNRPYRCKIRAPGFAHLQGLDFMSKHHMLADVVTIIGTQDIVSGEVDR NDUS3 Vigna radiata 0.022806779 1 LEVO MDNQSIFKYSWETLPKKWVKKMERSEHGNRFDTKTDYLFQLLCFLKLHTYTRVQVLIDICGVDYPSRKRRFEVVYNLLST RYNSRIRVQTSADEVTRISSVVSLFPSAGWWEREVWDMFGVSSINHPDLRRILTDYGFEGHPLRKDFPLSGYVEVRYDDP EKRVVSEPIEMTQEFRYFDFASPWEQRSDG NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial Vigna radiata 0.016435736 1 LEVO MANTLQRALRATMARRFSTQALVETKPGEIGMVSGIPQEHLRRRVVIYSPARTASQQGSGKVGRWKINFLSTQKWENPLM GWTSTGDPYAHVGDSALTFDSAEAAKAFAEKHGWEYSVKKRHTPLLKVKSYADNFKWKGFPKPAEE A0A1S3UIW7 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial Vigna radiata 0.011582296 1 LEVO MASSVLRNLMRFSSPRNTSTRSFSLVTSQISNHTAKWMQDTSKKSPMELINEVPPIKVEGRIVACEGDTNPALGHPIEFI CLDLPEPAVCKYCGLRYVQDHHH A0A1S3VYF3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial Vigna radiata 0.023710473 1 LEVO MALLSRASSRIYQVHSYQRALSLHTTLPALNASTSTHTPTPYAPPPPPSASSPVGVSKAAEFVISKVDDLMNWARRGSIW PMTFGLACCAVEMMHTGAARYDLDRFGIIFRPSPRQSDCMIVAGTLTNKMAPALRKVYDQMPEPRWVISMGSCANGGGYY HYSYSVVRGCDRIVPVDIYVPGCPPTAEALLYGLLQLQKKINRRKDFLHWWTK A0A1S3U8J5 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial Vigna radiata 0.025545009999999996 1 LEVO MAAILARKSLLALRARQLAVSGQGLHSSQSYGLRLSAHSFSTKLEDEQREQLAKEISKDWSSVFERSINTLFLTEMVRGL MLTLKYFFETKVTINYPFEKGPLSPRFRGEHALRRYPTGEERCIACKLCEAICPAQAITIEAEEREDGSRRTTRYDIDMT KCIYCGFCQEACPVDAIVEGPNFEFATETHEELLYDKEKLLENGDRWETEIAENLRSESLYR A0A1S3VGS8 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial Vigna radiata 0.053817582 1 LEVO MRGILSLRSALVQHRSEKLGLGLRQFSTQGASTPTSPQPPPPPASPQPPPPPPPPEKTHFGGLKDEDRIFTNLYGLHDPF LKGAMKRGDWYRTKDLVIKGTDWIVNEMKKSGLRGRGGAGFPSGLKWSFMPKVSDGRPSYLVVNADESEPGTCKDREIMR HDPHKLLEGCLIAGVGMRATAAYIYIRGEYVNERKNLEKARQEAYAAGLLGKNACGSGYDFDVHIHFGAGAYICGEETAL LESLEGKQGKPRLKPPFPANAGLYGCPTTVTNVETVAVSPTILRRGPEWFAGFGRKNNAGTKLFCVSGHVNKPCTVEEEM SIPLKELIERHCGGVRGGWDNLLAVIPGGSSVPLLPKSICDDVLMDYDALKAVQSGLGTAAVIVMDKSTDVVDAIARLSY FYKHESCGQCTPCREGTGWLWTIMERMKVGNAKLEEIDMLQELTKQIEGHTICALGDAAAWPVQGLIRHFRPELERRIRE NAERELLQATG A0A1S3V7V2 1.6.99.3 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial Vigna radiata 0.027992949 1 LEVO MLARLAANRFNEIRHIFRQPSRAFSTALNYHLDSPDNNPNLPWEFTEPNKAKVTEILSHYPSNYKQSAVIPLLDLAQQQH GGWLPVSAMNAVANIIEVPPIRVYEVATFYSMFNRAKVGKYHLLVCGTTPCMIRGSRGIEEALLKHLGVKRNEVTPDGLF SVGEMECMGCCVNAPMITVADYSNGSEGYTYNYYEDVTPEKVVEIVEKLRKGEKPPHGTQNPLRIRSGPEGGNTTLLGEP KPPPCRDLDAC A0A1S3U769 NU1M Vigna radiata 0.035651366999999996 1 LEVO MYIAVPAEILGIILPLLLGVAFLVLAERKVMAFVQRRKGPDVVGSFGLLQPLADGLKLILKEPISPSSANFSLFRMAPVA TFMLSLVAWAVVPFDYGMVLSDSNIGLLYLFAISSLGVYGIITAGWSSNSKYAFLGALRSAAQMVSYEVSIGLILITVLI CVGSCNLSEIVMAQKQIWFGIPLFPVLVMFFISCLAETNRAPFDLPEAEAESVAGYNVEYSSMGSALFFLGEYANMILMS GLCTSLSLGGWLPILDLPIFKRIPGSIWFSIKVILFLFLYIWVRAAFPRYRYDQLMGLGWKVFLPLSLAWVVAVSGVSVT FPWLP NU2M Vigna radiata 0.053900663999999994 1 LEVO MFNLFLAVYPEIFIINATFILLIHGVVFSTSKKYDYPPLVSNVGWLGLLSVLITLLLLAAGAPLLTIAHLFRNNLFRRDN FTYFCQILLLLSTAGTISMCFDFFEQERFDAFEFIVLILLSTCSMLFMISAYDSIAMYLAIELQSLCFYVMAASKRKSEF STEAGLKYLILGAFSSGILLFGCSMIYGSTGATHFDQLAKILTGYEITGARSSGIFMGILFIAVGSLFKITAVPFHMWAP DIYEGSPTPVTAFLSIAPKISIFANISRVSIYGSYGATLQQIFCFCSIASMILGALAAMAQTKVKRLLAYSSIGHVGYIC TGFSCGTIEGIQSLLIGIFIYALMTIDAFAIVLALRQTRVKYIADLGALAKTNPILAITFSITMFSYVGIPPLAGFCSKF YLFFAALGCGAYFLAPVGVVTSVIGCFYYIRLAKRMFFDTPRTWILYEPMDRDKSLLLAMTSSFITLFFPYPSPLFSVTH QMALSLYL NU3M Vigna radiata 0.013507715 1 LEVO MSEFAPICIYLVISLLVSLILLGLPFLFASNSSTYPEKLSAYECGFDPFGDARSRFDIRFYLVSILFIIFDPEVTFSFPW AVSLNKIDPFGSWSMMAFLLILTIGSLYEWKRGALDWE NU4L Vigna radiata 0.011082356 1 LEVO MDPIKYFTFSMIIFILGIRGILLNRRNILIMLMSIELMLLAVNSNFLVFSVSLDDMMGQSFALLVLTVAAAESAIGLAIF VITFRVRGTIAVEFINSIQG NU6M Vigna radiata 0.023484177999999998 1 LEVO MILSVLSSLALVSGLMVVRAKNPVHSVLFFILVFCDTSGLLLLLGLDFSAMIFLVVYIGAIAVLFLFVVMMFHIQIAEIH EEVLRYLPVSGIIGLILWWEMFFILDNETIPLLPTQINTTSLIYTVYAGKVRSWTNLETLGNLLYTYYFVWFLVPSLILL VAMIGAIVLTMHRTTKVKRQDVFRRNAIDFRRTIMRRTTDPLTID NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 Vigna radiata 0.007357572 1 LEVO MNLRWMEAVLPLGIIAGMLCVMGNAQYYIHKAAHGRPKHIGNDLWDVAMERRDKKLHEQAASSSN A0A1S3TU57 uncharacterized protein LOC106754061 Vigna radiata 0.006695044 1 LEVO MAVMEKLKMFVVQEPVVAASCLIAGFGLFLPAVVRPILDSYQATKQPPQPALSDVVAGMTGKK A0A1S3TCK0 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B Vigna radiata 0.012022893 1 LEVO MASAVDASGNPIPSSSVLMASSKHIGIRCHSENLDFLKCKKKDPNPEKCLDKGRDVTRCVLGLLKDLHQKCTKEMDDYVG CMYYHTNEFDLCRKEQQAFEKKCSLE A0A1S3VVN6 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A Vigna radiata 0.0161896 1 LEVO MTEAYIRNKPGMVSVKDMPVLQDGPPPGGFAPVRFARRIPNKGPSAVAIFLAAFGTFSWGMYQVGQGNKIRRALKEEKYA ARRSILPVLQAEEDERFVREWHKYLAYEAEVMKDVPGWKVGESVYNSGRWVPPASGELRPDIW A0A1S3UYW0 Unknown Peptide Vigna radiata 0.002145636 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) Unknown Peptide Vigna radiata 0.0036775239999999997 1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) NDUC2 Vigna radiata 0.009130512 1 LEVO MVLSATTIGALLGLGTQMYSNALRKLPYMRHPWEHVVGMGLGAVFVNQLLKWEAQVEQDLDKMLEKAKAANERRYIDGDD D A0A1S3UPL8 Protein At2g27730, mitochondrial Vigna radiata 0.012172665999999999 1 LEVO MAARVAARYGSRRLFSSGSGKILSEEEKAAENAYFKKAEQDKLEKLARKGPQPEASSGGSVIDAKPSGSGHTGASAERVS TDKHRNYAVVAGTITILGALGWYLKGTAKKPEVQD A0A1S3TGE7 serine/arginine-rich-splicing factor SR34 isoform X2 Vigna radiata 0.045640944999999995 1 LEVO MASGWGITGNKGRCYDFWMDFSECMSRCREPKDCGLLREDYLECLHHSKEFQRRNRIYKEEQRKIRAAAKKAKDDGVVKE HHYLHGNTTDSNPHLSKVKKMSRRSSRTVYVGNLPGDIREREVEDLFLKYGHITHIDLKVPPRPPGYAFVEFEDAQDAED AIRGRDGYDFDGHRLRVEPAHGGRGHSSSRDRHSSHSNGRAGRGVSRRSEYRVLVTGLPSSASWQDLKDHMRKAGDVCFS QVFHDGRGTTGIVDYTNYDDMKYAIKKLDDSEFRNAFSKGYVRVREYDSRRDSSRSPSRGPSHSRGRSYSRSRSRSRSYS RDRSQSKSPKGKSSQRSPPAKSPSRSPAARSRSRSRSRSLSGSRSRSRSPLPPRNKSPKRGSASRSPSRSRSRSKSLSR A0A1S3TQ33 NDUX1 Vigna radiata 0.01094954 1 LEVO MNTDITASTKPEYPVVDRNPPFTKVVGNFSTLDYLRFVTITGVSVTVGYLSGIKPGIRGPSMVTGGLIGVMGGFMYAYQN SAGRLMGFFPNDDEVARHNKK A0A1S3VI15 gamma carbonic anhydrase 1, mitochondrial Vigna radiata 0.029333197 1 LEVO MGTLGRAFYAVGFWIRETGQAIDRLGSRLQGNYLFQEQLSRHRPLMNLFDKYPSVHKDAFVAPSASLLGDVHVGPASSIW YGCVLRGDVNGIVIGSGTNIQDNSLVHVAKSNLTGKVLPTIIGDNVTVGHSAVLQGCTVEDEAFIGMGATLLDGVYVEKH AMVAAGALVRQNTRIPYGEVWGGNPAKFLRKLTEDEMAFFSQSALNYSNLAQAHAAENAKELEETEFVKVLHKKFAPRGE EYDSILDGGQETPAKLNLQDNVLLDKAPKA A0A1S3VT00 gamma carbonic anhydrase 1, mitochondrial-like Vigna radiata 0.029780861 1 LEVO MGTLGRAIYSVGFWIRETGQAIDRLGSRLQGGYFFQEQLSRHRTLMNIFDKAPVVDKDVFVAPSASVIGDVQVGRGSSIW YGCVLRGDVNSIRVGSGTNIQDNSLVHVAKSNLSGKVLPTVIGDNVTVGHSAVLHGCTVEDEAFVGMGAVLLDGVVVEKN AMVAAGALVRQNTRIPSGEVWAGNPAKFLRKLSNEEITFISQSAINYTNLAQVHAAENSKSYDEIEFEKVLRKKYARKDE EYDSMLGVVREIPPELILPDNVLPDKAEKALQK A0A1S3U544 gamma carbonic anhydrase-like 2, mitochondrial Vigna radiata 0.028268359 1 LEVO MANLARFSKRALRSAHSLVRHAQSQVQPQLFAEERAFSTEAAKSITPSPDRVKWDYRGQRKIIPLGQWLPKVAVDAYVAP NVVLAGQVTVWDGASVWPGCVLRGDLNKISIGFCSNVQERSVLHAAWTSPTGLPADTSIERYVTIGAYSLLRSCTIEPEC IIGQHSILMEGSLVETQSILEAGSVVPPGRRIPSGELWAGNPARFVRTLTHEEILEIPKLAVAINDLSRDHYSEFLPYST VYLEVEKFKKSLGISV A0A1S3UI49 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 0.0007434049999999999 1 NAP 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007901449999999999 6 PC1 IRON/SULFUR CLUSTER 0.00035163999999999996 6 SF4 FE2/S2 (INORGANIC) CLUSTER 0.00017581999999999998 2 FES ZINC ION 6.5409e-05 2 ZN FLAVIN MONONUCLEOTIDE 0.00045634399999999997 1 FMN singleParticle particle 6 7.8 20.0 HEPES HEPES 150.0 NaCl sodium chloride 0.1 digitonin digitonin 1.0 edta EDTA Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE 30

30 mA

ETHANE FEI VITROBOT MARK III

Blotted for 9 seconds at 100% humidity, 15 degrees C..

Extracted from V. radiata mitochondrial membranes with digitonin, exchanged into amphipole A8-35, purified on sucrose gradient.

TFS KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 (6k x 4k) 1 9816 3.0 86.4 1 190951 CTFFIND PHASE FLIPPING AND AMPLITUDE CORRECTION Ab initio 1 C1 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF RELION 34407 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION 3 RELION OTHER REAL