8IC2: NADH-ubiquinone oxidoreductase chain 3

Respiratory complex CI:CIII2, type I, PERK -/- mouse under cold temperature. Determined by electron microscopy at 6.3 Å resolution. Released 18 Sept 2024.

Method
Electron microscopy
Resolution
6.3 Å
Organism
Mus musculus
Chains
66
Atoms
97,017
Mol. weight
1627.36 kDa
Ligands
UQ1, 3PE, FES, FMN
Released
18 Sept 2024

Explore 8IC2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IC2 contains 659 α-helices and 308 β-strands across 66 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 a: 3 helices, 0 β-strands

ElementResiduesLengthSheet
α-helix5-3026
α-helix35-373
α-helix42-5413
Chain A: 6 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-2322
α-helix24-263
α-helix53-7220
α-helix75-784
α-helix84-10421
α-helix105-1095
Chain Aa: 19 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix45-473
β-strand49-52418
β-strand58-63618
β-strand68-75818
α-helix79-813
α-helix89-968
β-strand101119
α-helix107-1159
β-strand119-124618
β-strand129-136818
α-helix140-15112
β-strand154119
α-helix158-17518
α-helix179-19113
α-helix205-2095
α-helix213-22311
α-helix226-2283
β-strand229-235718
α-helix239-24810
β-strand274-278520
β-strand285-292820
α-helix300-31011
β-strand340-348920
β-strand351-3601020
α-helix362-3643
α-helix365-38117
α-helix385-40218
α-helix406-41914
α-helix426-4349
α-helix438-44811
β-strand455-460620
α-helix468-4747
Chain AA: 19 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix45-473
β-strand49-50291
β-strand58-63691
β-strand68-75891
α-helix79-813
α-helix89-968
β-strand101192
α-helix107-1159
β-strand119-124691
β-strand129-136891
α-helix140-15112
β-strand154192
α-helix158-17518
α-helix179-19113
α-helix205-2095
α-helix213-22311
α-helix226-2283
β-strand229-235791
α-helix239-24810
β-strand274-279693
β-strand285-292893
α-helix300-31112
β-strand344-348593
β-strand351-3601093
α-helix364-38118
α-helix385-39612
α-helix397-4015
α-helix406-41914
α-helix426-4349
α-helix438-44811
β-strand455-460693
α-helix468-4747
Chain Ab: 19 helices, 17 β-strands
ElementResiduesLengthSheet
β-strand39-4243
β-strand48-5253
β-strand58-6583
α-helix69-713
α-helix79-857
β-strand91130
β-strand94130
α-helix96-10510
β-strand109-11463
β-strand119-12683
α-helix130-14213
β-strand144130
α-helix148-16518
α-helix169-18113
β-strand182131
α-helix202-21211
α-helix215-2173
β-strand218-22363
α-helix227-23610
α-helix246-2516
β-strand253131
β-strand256-261632
β-strand266-2751032
α-helix276-2772
α-helix281-29313
β-strand299118
α-helix308-3147
β-strand321-3301032
β-strand333-3431132
α-helix347-36216
α-helix368-38619
α-helix389-40315
α-helix409-41810
α-helix421-43313
α-helix4351
β-strand436-442732
Chain AB: 19 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand39-42494
β-strand48-52594
β-strand58-65894
α-helix69-713
α-helix79-846
α-helix85-884
β-strand91195
α-helix96-10510
β-strand109-114694
β-strand119-126894
α-helix130-14213
β-strand144195
α-helix148-16518
α-helix169-18113
β-strand182196
α-helix202-21211
α-helix215-2173
β-strand218-223694
α-helix227-23610
α-helix246-2516
β-strand253196
β-strand256-261697
β-strand266-2751097
α-helix281-29313
β-strand299191
α-helix308-3147
β-strand321-3301097
β-strand333-3431197
α-helix347-36216
α-helix368-38619
α-helix389-40315
α-helix409-41810
α-helix421-43313
α-helix4351
β-strand436-442797
Chain Ac: 23 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix9-146
α-helix15-195
β-strand23-24246
α-helix29-324
α-helix33-5220
α-helix62-7110
α-helix76-10328
α-helix106-1083
α-helix110-13223
β-strand136147
α-helix137-15014
α-helix157-1659
α-helix172-20130
α-helix213-2153
β-strand217-218246
α-helix225-24319
α-helix253-2564
β-strand258147
α-helix263-2653
α-helix272-2743
α-helix275-2839
α-helix287-30317
α-helix304-3063
α-helix319-34022
α-helix347-36014
α-helix361-3655
α-helix366-37611
Chain AC: 22 helices, 4 β-strands
ElementResiduesLengthSheet
α-helix11-188
β-strand23-24298
α-helix29-324
α-helix33-5220
α-helix62-7110
α-helix76-10328
α-helix106-1083
α-helix110-13223
β-strand136199
α-helix137-15115
α-helix157-1659
α-helix172-20130
α-helix213-2153
β-strand217-218298
α-helix225-24319
α-helix253-2564
β-strand258199
α-helix263-2653
α-helix272-2743
α-helix275-2839
α-helix287-30317
α-helix304-3074
α-helix319-34022
α-helix347-36014
α-helix361-3655
α-helix366-37611

56 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-ubiquinone oxidoreductase chain 3Aprotein115Mus musculusP03899 (AlphaFold model)
NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrialBprotein224Mus 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, mitochondrialEprotein248Mus musculusQ9D6J6
NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrialFprotein464Mus musculusQ91YT0
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialGprotein727Mus musculusQ91VD9
NADH-ubiquinone oxidoreductase chain 1Hprotein318Mus musculusP03888
NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrialIprotein212Mus musculusQ8K3J1
NADH-ubiquinone oxidoreductase chain 6Jprotein172Mus musculusP03925
NADH-ubiquinone oxidoreductase chain 4LKprotein98Mus musculusP03903
NADH-ubiquinone oxidoreductase chain 5Lprotein607Mus musculusP03921

42 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>8IC2_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE
Sequence of entity 2 (B), FASTA
>8IC2_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR
Sequence of entity 3 (C), FASTA
>8IC2_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 4 (D), FASTA
>8IC2_4 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains D)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR
Sequence of entity 5 (E), FASTA
>8IC2_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL
Sequence of entity 6 (F), FASTA
>8IC2_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS
Sequence of entity 7 (G), FASTA
>8IC2_7 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains G)
MLRIPIKRALIGLSNSPKGYVRTTGTAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQI
PRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFL
LANHPLDCPICDQGGECDLQDQSMMFGSDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCT
RCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNVIDICPVGALTSKPYAFTA
RPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQ
RLTEPMVRNEKGLLTYTSWEDALSRVAGMLQNFEGNAVAAIAGGLVDAEALVALKDLLNK
VDSDNLCTEEIFPTEGAGTDLRSNYLLNTTIAGVEEADVVLLVGTNPRFEAPLFNARIRK
SWLHNDLKVALIGSPVDLTYRYDHLGDSPKILQDIASGRHSFCEVLKDAKKPMVVLGSSA
LQRDDGAAILVAVSNMVQKIRVTTGVAAEWKVMNILHRIASQVAALDLGYKPGVEAIRKN
PPKMLFLLGADGGCITRQDLPKDCFIVYQGHHGDVGAPMADVILPGAAYTEKSATYVNTE
GRAQQTKVAVTPPGLAREDWKIIRALSEIAGITLPYDTLDQVRNRLEEVSPNLVRYDDIE
ETNYFQQASELAKLVNQEVLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGAQA
VEEPSIC
Sequence of entity 8 (H), FASTA
>8IC2_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM
Sequence of entity 9 (I), FASTA
>8IC2_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 10 (J), FASTA
>8IC2_10 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD
Sequence of entity 11 (K), FASTA
>8IC2_11 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC
Sequence of entity 12 (L), FASTA
>8IC2_12 NADH-ubiquinone oxidoreductase chain 5 (chains L)
MNIFTTSILLIFILLLSPILISMSNLIKHINFPLYTTTSIKFSFIISLLPLLMFFHNNME
YMITTWHWVTMNSMELKMSFKTDFFSILFTSVALFVTWSIMQFSSWYMHSDPNINRFIKY
LTLFLITMLILTSANNMFQLFIGWEGVGIMSFLLIGWWYGRTDANTAALQAILYNRIGDI
GFILAMVWFSLNMNSWELQQIMFSNNNDNLIPLMGLLIAATGKSAQFGLHPWLPSAMEGP
TPVSALLHSSTMVVAGIFLLVRFHPLTTNNNFILTTMLCLGALTTLFTAICALTQNDIKK
IIAFSTSSQLGLMMVTLGMNQPHLAFLHICTHAFFKAMLFMCSGSIIHSLADEQDIRKMG
NITKIMPFTSSCLVIGSLALTGMPFLTGFYSKDLIIEAINTCNTNAWALLITLIATSMTA
MYSMRIIYFVTMTKPRFPPLISINENDPDLMNPIKRLAFGSIFAGFVISYNIPPTSIPVL
TMPWFLKTTALIISVLGFLIALELNNLTMKLSMNKANPYSSFSTLLGFFPSIIHRITPMK
SLNLSLKTSLTLLDLIWLEKTIPKSTSTLHTNMTTLTTNQKGLIKLYFMSFLINIILIII
LYSINLE

Ligands and cofactors

IDNameFormulaCopies
UQ1Ubiquinone-1C14 H18 O41
3PE1,2-Distearoyl-sn-glycerophosphoethanolamineC41 H82 N O8 P14
FESFE2/S2 (inorganic) clusterFe2 S22
FMNFlavin mononucleotideC17 H21 N4 O9 P1
UQ9Ubiquinone-9C54 H82 O41
CDLCardiolipinC81 H156 O17 P29
ZNZinc ionZn2
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P21
NDPNADPH dihydro-nicotinamide-adenine-dinucleotide phosphateC21 H30 N7 O17 P31
EHZ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]prop…C25 H49 N2 O9 P S2
HEMProtoporphyrin IX containing FEC34 H32 Fe N4 O44
UQ65-(3,7,11,15,19,23-hexamethyl-tetracosa-2,6,10,14,18,22-hexaenyl)-2,3-dimethoxy…C39 H60 O42
HECHeme CC34 H36 Fe N4 O42
U10Ubiquinone-10C59 H90 O41
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P2
SF4Iron/sulfur clusterFe4 S46

Primary citation

Structural basis of respiratory complex adaptation to cold temperatures. Shin, Y.C., Latorre-Muro, P., Djurabekova, A. et al. Cell (2024) 187:6584. DOI 10.1016/j.cell.2024.09.029 · PubMed

Other PDB entries of the same protein (UniProt P03899 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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