8RGQ: Open Complex I from murine liver

Open Complex I from murine liver. Determined by electron microscopy at 3.0 Å resolution. Released 24 Apr 2024.

Method
Electron microscopy
Resolution
3.0 Å
Organism
Mus musculus
Chains
45
Atoms
67,118
Mol. weight
1076.67 kDa
Ligands
SF4, 3PE, PC1, FES
Released
24 Apr 2024

Explore 8RGQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RGQ contains 461 α-helices and 198 β-strands across 45 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 1: 25 helices, 19 β-strands

ElementResiduesLengthSheet
α-helix33-397
α-helix45-517
α-helix53-6311
β-strand66115
β-strand74115
α-helix75-806
β-strand92-97616
α-helix106-1138
α-helix115-12915
β-strand133-138616
α-helix143-15917
α-helix166-1683
β-strand174-179616
α-helix185-1873
α-helix189-1979
α-helix202-2054
α-helix2091
α-helix215-2173
β-strand220-224516
α-helix225-23713
α-helix239-2446
β-strand246-247217
β-strand250-251217
β-strand253-260818
β-strand262119
β-strand266-271618
β-strand275120
α-helix276-2794
α-helix280-2845
β-strand287119
β-strand294-298518
β-strand299121
β-strand301121
α-helix305-3062
β-strand307-308218
α-helix309-3124
β-strand316120
α-helix319-3246
β-strand333-338618
α-helix343-35715
α-helix363-38119
α-helix387-39913
α-helix407-42115
α-helix423-43715
Chain 2: 12 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix25-3713
α-helix391
β-strand40113
α-helix43-464
α-helix47-5812
α-helix63-7311
α-helix77-8610
β-strand98-103614
α-helix106-1105
α-helix113-12412
β-strand131114
β-strand137-142614
β-strand154-156314
β-strand159-162414
α-helix166-17813
β-strand185-186214
α-helix1951
α-helix205-2062
α-helix213-2142
Chain 3: 35 helices, 37 β-strands
ElementResiduesLengthSheet
β-strand9-13522
β-strand16-20522
β-strand25123
α-helix26-338
α-helix47-482
β-strand56-57224
β-strand58-59222
β-strand66-67224
α-helix711
β-strand72123
α-helix731
β-strand78-80322
α-helix84-10017
α-helix115-1239
α-helix133-1353
β-strand146-148325
α-helix150-1523
α-helix158-1625
α-helix163-1675
β-strand173-175326
α-helix178-1803
β-strand182-184326
α-helix198-2025
β-strand208-210325
β-strand223-228627
β-strand237-243727
β-strand246-252727
β-strand255128
β-strand260128
α-helix265-2695
α-helix271-2755
β-strand278129
β-strand283-285330
β-strand291-293330
α-helix296-30914
α-helix312-3143
β-strand315-319530
α-helix325-33713
β-strand343-345330
β-strand358131
α-helix359-3624
β-strand364132
α-helix367-3737
β-strand376-380532
α-helix384-3874
α-helix389-40113
β-strand405-409532
β-strand420-423432
α-helix427-4348
α-helix438-4458
β-strand449-454632
α-helix455-4584
α-helix463-48119
β-strand490-493432
α-helix497-5059
α-helix5071
β-strand508-509230
α-helix512-5165
β-strand521-525530
β-strand542-547630
β-strand549129
β-strand559-562430
β-strand571-574433
β-strand580-583433
α-helix584-5852
α-helix596-60712
α-helix616-62611
β-strand633133
α-helix642-65110
α-helix668-6725
α-helix676-6805
α-helix682-69211
Chain 6: 11 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix35-5319
β-strand57-6151
α-helix64-7310
α-helix79-824
α-helix90-923
β-strand95-9951
β-strand10312
α-helix107-11610
β-strand122-12651
α-helix128-1325
α-helix134-1363
β-strand14212
α-helix146-1483
β-strand154-15631
α-helix161-1622
α-helix163-17816
α-helix182-1876
Chain 7: 7 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand3-4246
α-helix91
β-strand10-11246
α-helix121
α-helix23-275
α-helix40-456
α-helix48-492
β-strand50-52347
β-strand56-59448
α-helix64-663
α-helix68-703
β-strand71-74448
β-strand82-83247
β-strand90-93447
Chain 9: 7 helices, 10 β-strands
ElementResiduesLengthSheet
β-strand2134
β-strand3-4211
α-helix16-2813
α-helix30-4415
β-strand67-69335
β-strand71136
β-strand77136
α-helix84-885
β-strand94-100737
β-strand106-114937
α-helix123-1275
β-strand133-135335
β-strand14311
α-helix147-1493
β-strand150-151237
α-helix153-16210
α-helix164-17411
Chain a: 5 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-54
α-helix6-3025
α-helix35-384
α-helix42-5514
α-helix66-683
Chain A: 4 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-2322
α-helix53-7220
α-helix75-784
α-helix84-10724

37 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial6protein224Mus musculusQ9DC70 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrialCprotein263Mus musculusQ9DCT2 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrialDprotein463Mus musculusQ91WD5 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial2protein248Mus musculusQ9D6J6 (AlphaFold model)
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial1protein464Mus musculusQ91YT0
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial3protein727Mus musculusQ91VD9
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial9protein212Mus musculusQ8K3J1
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrialPprotein377Mus musculusQ9DC69
NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrialQprotein175Mus musculusQ9CXZ1
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial7protein116Mus musculusP52503
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2Sprotein99Mus musculusQ9CQ75
Acyl carrier protein, mitochondrialT, Uprotein156Mus musculusQ9CR21

32 more molecules are not listed.

Sequence of entity 1 (6), FASTA
>8RGQ_1 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains 6)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR
Sequence of entity 2 (C), FASTA
>8RGQ_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 3 (D), FASTA
>8RGQ_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains D)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR
Sequence of entity 4 (2), FASTA
>8RGQ_4 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains 2)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL
Sequence of entity 5 (1), FASTA
>8RGQ_5 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains 1)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS
Sequence of entity 6 (3), FASTA
>8RGQ_6 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains 3)
MLRIPIKRALIGLSNSPKGYVRTTGTAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQI
PRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFL
LANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCT
RCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNVIDICPVGALTSKPYAFTA
RPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQ
RLTEPMVRNEKGLLTYTSWEDALSRVAGMLQNFEGNAVAAIAGGLVDAEALVALKDLLNK
VDSDNLCTEEIFPTEGAGTDLRSNYLLNTTIAGVEEADVVLLVGTNPRFEAPLFNARIRK
SWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGRHSFCEVLKDAKKPMVVLGSSA
LQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILHRIASQVAALDLGYKPGVEAIRKN
PPKMLFLLGADGGCITRQDLPKDCFIVYQGHHGDVGAPMADVILPGAAYTEKSATYVNTE
GRAQQTKVAVTPPGLAREDWKIIRALSEIAGITLPYDTLDQVRNRLEEVSPNLVRYDDIE
ETNYFQQASELAKLVNQEVLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGAQA
VEEPSIC
Sequence of entity 7 (9), FASTA
>8RGQ_7 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains 9)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 8 (P), FASTA
>8RGQ_8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains P)
MAAAVRFRVVRALPMSRPAITAAATSVFCGSSHRQLHHAVIPHGKGGRSSVSGVVATVFG
ATGFLGRYVVNHLGRMGSQVIIPYRCDVYDIMHLRLMGDLGQLTFLEWDARDKDSIRKAV
QHSNVVINLIGREWETRNFDFEDVFVNIPRAIAQASKEAGVERFIHVSHLNASMKSSSKS
LRSKAVGEKEVRSVFPEAIIIRPSDIFGREDRFLNHFANYRWFLAVPLVSLGFKTVKQPV
YVADVSKGIVNATKDPDAVGKTFAFTGPNRYLLFHLVKYIFGMTHRTFIPYPLPLFVYSW
IGKLFGLSPFEPWTTKDKVERIHISDVMPTDLPGLEDLGVQPTPLELKSIEVLRRHRTYR
WLSSEIEETKPAKTVNY
Sequence of entity 9 (Q), FASTA
>8RGQ_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains Q)
MAAVSISVSLRQAMLGRRAMATAAVSVCRVPSRLLSTSTWKLADNQTRDTQLITVDEKLD
ITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADP
LSNMVLTFSAKEDAIAFAEKNGWSYDVEEKKVPKPKSKSYGANFSWNKRTRVSTK
Sequence of entity 10 (7), FASTA
>8RGQ_10 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (chains 7)
MAAVLTFRRLLTLPRAARGFGVQVSPSGEKITHTGQVYDEKDYRRVRFVDRQKEVNENFA
IDLIAQQPVNEVEHRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH
Sequence of entity 11 (S), FASTA
>8RGQ_11 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains S)
MAAAAASRAVGAKLGLREIRVHLCQRSPGSQGVRDFIVQRYVELKKAHPNLPILIRECSE
VQPKLWARYAFGQEKTVSLNNLSADEVTRAMQNVLSGKA
Sequence of entity 12 (T, U), FASTA
>8RGQ_12 Acyl carrier protein, mitochondrial (chains T, U)
MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGT
VTHLCRQYSDAPPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE

Ligands and cofactors

IDNameFormulaCopies
SF4Iron/sulfur clusterFe4 S46
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P17
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P4
FESFE2/S2 (inorganic) clusterFe2 S22
FMNFlavin mononucleotideC17 H21 N4 O9 P1
NDPNADPH dihydro-nicotinamide-adenine-dinucleotide phosphateC21 H30 N7 O17 P31
ZNZinc ionZn1
ZMPS-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami…C25 H49 N2 O8 P S2
CDLCardiolipinC81 H156 O17 P26
DGT2'-deoxyguanosine-5'-triphosphateC10 H16 N5 O13 P31
MGMagnesium ionMg1

Water and common crystallization additives (K) are not listed.

Primary citation

SCAF1 drives the compositional diversity of mammalian respirasomes. Vercellino, I., Sazanov, L.A. Nat Struct Mol Biol (2024) 31:1061-1071. DOI 10.1038/s41594-024-01255-0 · PubMed

Other PDB entries of the same protein (UniProt Q9DC70 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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