7PSA: NADH-ubiquinone oxidoreductase chain 3
The acetogenin-bound complex I of Mus musculus resolved to 3.4 angstroms. Determined by electron microscopy at 3.4 Å resolution. Released 6 Apr 2022.
- Method
- Electron microscopy
- Resolution
- 3.4 Å
- Organism
- Mus musculus
- Chains
- 45
- Atoms
- 67,082
- Mol. weight
- 1072.89 kDa
- Ligands
- EHZ, ZN, NDP, ATP
- Released
- 6 Apr 2022
Explore 7PSA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7PSA contains 446 α-helices and 192 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: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 6-15 | 10 | |
| α-helix | 18-30 | 13 | |
| α-helix | 42-54 | 13 | |
Chain A: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 31-34 | 4 | |
| α-helix | 42-43 | 2 | |
| α-helix | 56-70 | 15 | |
| α-helix | 75-78 | 4 | |
| α-helix | 86-107 | 22 | |
| α-helix | 113-114 | 2 | |
Chain b: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-14 | 10 | |
| α-helix | 17-34 | 18 | |
| α-helix | 40-47 | 8 | |
| α-helix | 78-81 | 4 | |
Chain B: 12 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-52 | 17 | |
| β-strand | 58 | 1 | 1 |
| β-strand | 61 | 1 | 2 |
| α-helix | 66-73 | 8 | |
| α-helix | 80-82 | 3 | |
| β-strand | 87 | 1 | 1 |
| α-helix | 90-92 | 3 | |
| β-strand | 95-96 | 2 | 3 |
| β-strand | 99 | 1 | 2 |
| β-strand | 103 | 1 | 4 |
| α-helix | 107-116 | 10 | |
| α-helix | 118 | 1 | |
| β-strand | 122-123 | 2 | 3 |
| β-strand | 124-126 | 3 | 2 |
| α-helix | 128-131 | 4 | |
| 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 | 163-177 | 15 | |
| α-helix | 182-188 | 7 | |
Chain c: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| α-helix | 14-46 | 33 | |
Chain C: 6 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 11 | 1 | 5 |
| α-helix | 12-13 | 2 | |
| α-helix | 17-31 | 15 | |
| β-strand | 37-42 | 6 | 6 |
| β-strand | 48-52 | 5 | 6 |
| α-helix | 54-56 | 3 | |
| α-helix | 57-66 | 10 | |
| β-strand | 74-81 | 8 | 6 |
| β-strand | 91-97 | 7 | 6 |
| β-strand | 104-110 | 7 | 6 |
| β-strand | 112 | 1 | 7 |
| β-strand | 115 | 1 | 7 |
| β-strand | 117-118 | 2 | 8 |
| α-helix | 127-138 | 12 | |
| β-strand | 142-143 | 2 | 8 |
| β-strand | 172-177 | 6 | 9 |
| β-strand | 182-187 | 6 | 9 |
| β-strand | 190 | 1 | 10 |
| α-helix | 207-209 | 3 | |
Chain d: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-20 | 5 | |
| α-helix | 22-24 | 3 | |
| α-helix | 31-48 | 18 | |
| α-helix | 51-52 | 2 | |
| α-helix | 60-96 | 37 | |
| α-helix | 98-100 | 3 | |
| α-helix | 106-108 | 3 | |
Chain D: 25 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-12 | 5 | |
| α-helix | 30-32 | 3 | |
| α-helix | 42-44 | 3 | |
| β-strand | 47-51 | 5 | 11 |
| α-helix | 56-58 | 3 | |
| β-strand | 63-68 | 6 | 11 |
| β-strand | 72 | 1 | 12 |
| β-strand | 73-75 | 3 | 11 |
| β-strand | 78-79 | 2 | 11 |
| α-helix | 87-92 | 6 | |
| α-helix | 100-104 | 5 | |
| α-helix | 115-126 | 12 | |
| β-strand | 128 | 1 | 5 |
| α-helix | 132-161 | 30 | |
| α-helix | 165-184 | 20 | |
| β-strand | 198 | 1 | 13 |
| α-helix | 202-204 | 3 | |
| α-helix | 207-228 | 22 | |
| α-helix | 233-239 | 7 | |
| α-helix | 247-252 | 6 | |
| α-helix | 258-263 | 6 | |
| α-helix | 269-272 | 4 | |
| α-helix | 277-279 | 3 | |
| β-strand | 285-287 | 3 | 14 |
| α-helix | 293-316 | 24 | |
| β-strand | 324 | 1 | 13 |
| α-helix | 332-334 | 3 | |
| α-helix | 335-338 | 4 | |
| α-helix | 342-351 | 10 | |
| α-helix | 356-359 | 4 | |
| β-strand | 361-368 | 8 | 15 |
| β-strand | 373-380 | 8 | 15 |
| β-strand | 388-392 | 5 | 15 |
| α-helix | 394-400 | 7 | |
| α-helix | 402-405 | 4 | |
| β-strand | 410 | 1 | 12 |
| 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
>7PSA_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE
Sequence of entity 2 (B), FASTA
>7PSA_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR
Sequence of entity 3 (C), FASTA
>7PSA_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 4 (D), FASTA
>7PSA_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
>7PSA_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL
Sequence of entity 6 (F), FASTA
>7PSA_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS
Sequence of entity 7 (G), FASTA
>7PSA_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
>7PSA_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM
Sequence of entity 9 (I), FASTA
>7PSA_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 10 (J), FASTA
>7PSA_10 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD
Sequence of entity 11 (K), FASTA
>7PSA_11 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC
Sequence of entity 12 (L), FASTA
>7PSA_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 |
|---|
| 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 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 7 |
| 88I | (3~{S},5~{S})-5-methyl-3-[(13~{R})-13-oxidanyl-13-[(2~{R},5~{R})-5-[(2~{R},5~{R… | C37 H68 O6 | 1 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 9 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 4 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
Primary citation
Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I. Grba, D.N., Blaza, J.N., Bridges, H.R. et al. J Biol Chem (2022) 298:101602-101602. DOI 10.1016/j.jbc.2022.101602 · 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
- 8OLT 2.84 Å, Mitochondrial complex I from Mus musculus in the active state bound with piericidin A
- 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).
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