8OLT: NADH-ubiquinone oxidoreductase chain 3
Mitochondrial complex I from Mus musculus in the active state bound with piericidin A. Determined by electron microscopy at 2.84 Å resolution. Released 9 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 2.84 Å
- Organism
- Mus musculus
- Chains
- 45
- Atoms
- 68,075
- Mol. weight
- 1081.22 kDa
- Ligands
- MYR, EHZ, ZN, NDP
- Released
- 9 Aug 2023
Explore 8OLT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OLT contains 513 α-helices and 221 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 a: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 6-29 | 24 | |
| α-helix | 35-38 | 4 | |
| α-helix | 42-55 | 14 | |
| α-helix | 66-68 | 3 | |
Chain A: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 31-34 | 4 | |
| α-helix | 36-37 | 2 | |
| α-helix | 56-72 | 17 | |
| α-helix | 75-78 | 4 | |
| α-helix | 84-107 | 24 | |
| α-helix | 113-114 | 2 | |
Chain b: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 16-34 | 19 | |
| α-helix | 38-46 | 9 | |
| β-strand | 56-57 | 2 | 80 |
| α-helix | 78-81 | 4 | |
Chain B: 11 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-53 | 19 | |
| β-strand | 55 | 1 | 1 |
| β-strand | 57 | 1 | 2 |
| β-strand | 58 | 1 | 3 |
| α-helix | 65-73 | 9 | |
| α-helix | 79-82 | 4 | |
| β-strand | 84 | 1 | 1 |
| β-strand | 87 | 1 | 3 |
| β-strand | 95-99 | 5 | 2 |
| β-strand | 103 | 1 | 4 |
| α-helix | 107-115 | 9 | |
| α-helix | 118 | 1 | |
| β-strand | 122-126 | 5 | 2 |
| α-helix | 128-132 | 5 | |
| α-helix | 134-136 | 3 | |
| β-strand | 142 | 1 | 4 |
| α-helix | 146-148 | 3 | |
| β-strand | 154-156 | 3 | 2 |
| α-helix | 161-162 | 2 | |
| α-helix | 163-178 | 16 | |
| α-helix | 182-187 | 6 | |
Chain c: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| α-helix | 14-45 | 32 | |
Chain C: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11 | 1 | 5 |
| α-helix | 17-32 | 16 | |
| β-strand | 37-42 | 6 | 6 |
| β-strand | 48-52 | 5 | 6 |
| α-helix | 54-56 | 3 | |
| α-helix | 57-66 | 10 | |
| β-strand | 74-82 | 9 | 6 |
| β-strand | 90-98 | 9 | 6 |
| β-strand | 103-111 | 9 | 6 |
| α-helix | 116 | 1 | |
| β-strand | 117-118 | 2 | 7 |
| α-helix | 119 | 1 | |
| α-helix | 127-138 | 12 | |
| β-strand | 142-143 | 2 | 7 |
| α-helix | 154 | 1 | |
| β-strand | 172-177 | 6 | 8 |
| β-strand | 182-187 | 6 | 8 |
| β-strand | 190 | 1 | 9 |
| α-helix | 193-196 | 4 | |
| α-helix | 207-209 | 3 | |
| α-helix | 210-212 | 3 | |
Chain d: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 22-25 | 4 | |
| α-helix | 29-49 | 21 | |
| α-helix | 58-96 | 39 | |
| α-helix | 98-100 | 3 | |
| α-helix | 105-107 | 3 | |
| β-strand | 108 | 1 | 15 |
| α-helix | 114-116 | 3 | |
Chain D: 25 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
| α-helix | 12-14 | 3 | |
| β-strand | 18 | 1 | 10 |
| α-helix | 23-27 | 5 | |
| α-helix | 30-32 | 3 | |
| α-helix | 40-43 | 4 | |
| β-strand | 47-51 | 5 | 11 |
| β-strand | 63-69 | 7 | 11 |
| β-strand | 72-79 | 8 | 11 |
| α-helix | 87-91 | 5 | |
| α-helix | 100-104 | 5 | |
| α-helix | 111-126 | 16 | |
| β-strand | 128 | 1 | 5 |
| α-helix | 132-161 | 30 | |
| α-helix | 165-185 | 21 | |
| β-strand | 194-195 | 2 | 12 |
| β-strand | 198-199 | 2 | 12 |
| α-helix | 202-204 | 3 | |
| α-helix | 207-229 | 23 | |
| α-helix | 233-239 | 7 | |
| α-helix | 247-252 | 6 | |
| α-helix | 258-261 | 4 | |
| α-helix | 269-272 | 4 | |
| β-strand | 285-287 | 3 | 13 |
| α-helix | 293-317 | 25 | |
| α-helix | 318-320 | 3 | |
| β-strand | 324 | 1 | 12 |
| α-helix | 335-338 | 4 | |
| α-helix | 342-351 | 10 | |
| α-helix | 356-359 | 4 | |
| β-strand | 361-368 | 8 | 14 |
| β-strand | 373-380 | 8 | 14 |
| β-strand | 386-392 | 7 | 14 |
| α-helix | 394-400 | 7 | |
| α-helix | 402-405 | 4 | |
| β-strand | 410 | 1 | 11 |
| α-helix | 411-420 | 10 | |
| α-helix | 425-429 | 5 | |
37 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| NADH-ubiquinone oxidoreductase chain 3 | A | protein | 115 | Mus musculus | P03899 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | B | protein | 224 | Mus musculus | Q9DC70 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial | C | protein | 263 | Mus musculus | Q9DCT2 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | D | protein | 463 | Mus musculus | Q91WD5 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial | E | protein | 248 | Mus musculus | Q9D6J6 |
| NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial | F | protein | 464 | Mus musculus | Q91YT0 |
| NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial | G | protein | 727 | Mus musculus | Q91VD9 |
| NADH-ubiquinone oxidoreductase chain 1 | H | protein | 318 | Mus musculus | P03888 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | I | protein | 212 | Mus musculus | Q8K3J1 |
| NADH-ubiquinone oxidoreductase chain 6 | J | protein | 172 | Mus musculus | P03925 |
| NADH-ubiquinone oxidoreductase chain 4L | K | protein | 98 | Mus musculus | P03903 |
| NADH-ubiquinone oxidoreductase chain 5 | L | protein | 607 | Mus musculus | P03921 |
32 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8OLT_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE
Sequence of entity 2 (B), FASTA
>8OLT_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR
Sequence of entity 3 (C), FASTA
>8OLT_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 4 (D), FASTA
>8OLT_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
>8OLT_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL
Sequence of entity 6 (F), FASTA
>8OLT_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS
Sequence of entity 7 (G), FASTA
>8OLT_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
>8OLT_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM
Sequence of entity 9 (I), FASTA
>8OLT_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 10 (J), FASTA
>8OLT_10 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD
Sequence of entity 11 (K), FASTA
>8OLT_11 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC
Sequence of entity 12 (L), FASTA
>8OLT_12 NADH-ubiquinone oxidoreductase chain 5 (chains L)
MNIFTTSILLIFILLLSPILISMSNLIKHINFPLYTTTSIKFSFIISLLPLLMFFHNNME
YMITTWHWVTMNSMELKMSFKTDFFSILFTSVALFVTWSIMQFSSWYMHSDPNINRFIKY
LTLFLITMLILTSANNMFQLFIGWEGVGIMSFLLIGWWYGRTDANTAALQAILYNRIGDI
GFILAMVWFSLNMNSWELQQIMFSNNNDNLIPLMGLLIAATGKSAQFGLHPWLPSAMEGP
TPVSALLHSSTMVVAGIFLLVRFHPLTTNNNFILTTMLCLGALTTLFTAICALTQNDIKK
IIAFSTSSQLGLMMVTLGMNQPHLAFLHICTHAFFKAMLFMCSGSIIHSLADEQDIRKMG
NITKIMPFTSSCLVIGSLALTGMPFLTGFYSKDLIIEAINTCNTNAWALLITLIATSMTA
MYSMRIIYFVTMTKPRFPPLISINENDPDLMNPIKRLAFGSIFAGFVISYNIPPTSIPVL
TMPWFLKTTALIISVLGFLIALELNNLTMKLSMNKANPYSSFSTLLGFFPSIIHRITPMK
SLNLSLKTSLTLLDLIWLEKTIPKSTSTLHTNMTTLTTNQKGLIKLYFMSFLINIILIII
LYSINLE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MYR | Myristic acid | C14 H28 O2 | 1 |
| EHZ | ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]prop… | C25 H49 N2 O9 P S | 2 |
| ZN | Zinc ion | Zn | 1 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| GTP | Guanosine-5'-triphosphate | C10 H16 N5 O14 P3 | 1 |
| MG | Magnesium ion | Mg | 1 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 14 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 5 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| HQH | Piericidin A | C25 H37 N O4 | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 3 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 16 |
Water and common crystallization additives (NA) are not listed.
Primary citation
Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I. Grba, D.N., Chung, I., Bridges, H.R. et al. Sci Adv (2023) 9:eadi1359-eadi1359. DOI 10.1126/sciadv.adi1359 · PubMed
Other PDB entries of the same protein (UniProt P03899 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8OM1 2.39 Å, Mitochondrial complex I from Mus musculus in the active state
- 8RGR 2.9 Å, Closed Complex I from murine liver
- 6ZTQ 3.0 Å, Cryo-EM structure of respiratory complex I from Mus musculus inhibited by piericidin A…
- 8RGP 3.0 Å, Closed Complex I from murine brain
- 8RGQ 3.0 Å, Open Complex I from murine liver
- 7B93 3.04 Å, Cryo-EM structure of mitochondrial complex I from Mus musculus inhibited by IACS-2858 at…
- 6ZR2 3.1 Å, Cryo-EM structure of respiratory complex I in the active state from Mus musculus at 3.1 A
- 8RGT 3.1 Å, Open Complex I from murine brain
- 8XNL 3.1 Å, Respiratory complex Peripheral Arm of CI, close form A, focus-refined map of type I,…
- 7AK5 3.17 Å, Cryo-EM structure of respiratory complex I in the deactive state from Mus musculus at…
- 8CA3 3.2 Å, Cryo-EM structure NDUFS4 knockout complex I from Mus musculus heart (Class 2).
- 8IAP 3.2 Å, Respiratory complex Peripheral Arm of CI, focus-refined map of type I, Wild type mouse…
Browse structure collections
About this viewer
MolViewer shows 8OLT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.