8UCA: NADH-ubiquinone oxidoreductase chain 3
Formation of I2+III2 supercomplex rescues respiratory chain defects. Determined by electron microscopy at 3.7 Å resolution. Released 15 Jan 2025.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Mus musculus
- Chains
- 111
- Atoms
- 162,102
- Mol. weight
- 2577.85 kDa
- Ligands
- HEC, FES, SF4, FMN
- Released
- 15 Jan 2025
Explore 8UCA in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8UCA contains 1,048 α-helices and 473 β-strands across 111 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: 14 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-31 | 29 | |
| α-helix | 47-55 | 9 | |
| α-helix | 59-61 | 3 | |
| α-helix | 68-84 | 17 | |
| α-helix | 102-122 | 21 | |
| α-helix | 126-153 | 28 | |
| α-helix | 163-168 | 6 | |
| α-helix | 179-193 | 15 | |
| α-helix | 210-212 | 3 | |
| α-helix | 219-241 | 23 | |
| α-helix | 252-274 | 23 | |
| α-helix | 282-291 | 10 | |
| α-helix | 294-310 | 17 | |
| α-helix | 314-316 | 3 | |
Chain 1a: 16 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-31 | 29 | |
| α-helix | 47-57 | 11 | |
| α-helix | 59-60 | 2 | |
| α-helix | 68-83 | 16 | |
| α-helix | 101-111 | 11 | |
| α-helix | 115-122 | 8 | |
| α-helix | 126-152 | 27 | |
| α-helix | 162-165 | 4 | |
| α-helix | 179-193 | 15 | |
| α-helix | 217-242 | 26 | |
| α-helix | 252-276 | 25 | |
| α-helix | 278-279 | 2 | |
| α-helix | 282-287 | 6 | |
| α-helix | 288-293 | 6 | |
| α-helix | 294-310 | 17 | |
| α-helix | 314-316 | 3 | |
Chain 2: 25 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
| α-helix | 26-45 | 20 | |
| α-helix | 50-80 | 31 | |
| α-helix | 92-106 | 15 | |
| α-helix | 109-111 | 3 | |
| α-helix | 114-120 | 7 | |
| α-helix | 124-128 | 5 | |
| α-helix | 129-133 | 5 | |
| α-helix | 137-144 | 8 | |
| α-helix | 151-166 | 16 | |
| β-strand | 172 | 1 | 16 |
| β-strand | 174 | 1 | 78 |
| α-helix | 175-192 | 18 | |
| α-helix | 198-222 | 25 | |
| β-strand | 226 | 1 | 78 |
| α-helix | 227-231 | 5 | |
| α-helix | 233-236 | 4 | |
| α-helix | 238-240 | 3 | |
| α-helix | 241-252 | 12 | |
| α-helix | 260-272 | 13 | |
| α-helix | 276-285 | 10 | |
| α-helix | 287-297 | 11 | |
| α-helix | 298-302 | 5 | |
| α-helix | 309-311 | 3 | |
| α-helix | 312-316 | 5 | |
| α-helix | 324-334 | 11 | |
| α-helix | 337-339 | 3 | |
| α-helix | 340-343 | 4 | |
Chain 2a: 19 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
| α-helix | 26-44 | 19 | |
| α-helix | 50-80 | 31 | |
| α-helix | 92-106 | 15 | |
| α-helix | 114-121 | 8 | |
| α-helix | 124-131 | 8 | |
| α-helix | 139-142 | 4 | |
| α-helix | 151-167 | 17 | |
| β-strand | 172 | 1 | 116 |
| β-strand | 174 | 1 | 139 |
| α-helix | 175-192 | 18 | |
| α-helix | 198-222 | 25 | |
| β-strand | 226 | 1 | 139 |
| α-helix | 227-231 | 5 | |
| α-helix | 233-236 | 4 | |
| α-helix | 241-252 | 12 | |
| α-helix | 260-271 | 12 | |
| α-helix | 277-284 | 8 | |
| α-helix | 287-300 | 14 | |
| α-helix | 304-306 | 3 | |
| β-strand | 307-308 | 2 | 140 |
| α-helix | 311-316 | 6 | |
| α-helix | 324-334 | 11 | |
Chain 3: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
| α-helix | 36-37 | 2 | |
| β-strand | 38 | 1 | 1 |
| β-strand | 41 | 1 | 1 |
| α-helix | 56-72 | 17 | |
| α-helix | 75-78 | 4 | |
| α-helix | 84-108 | 25 | |
Chain 3a: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-22 | 20 | |
| α-helix | 56-72 | 17 | |
| α-helix | 75-78 | 4 | |
| α-helix | 84-107 | 24 | |
Chain 3A: 24 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-43 | 6 | |
| α-helix | 46-47 | 2 | |
| β-strand | 49-52 | 4 | 23 |
| β-strand | 58-61 | 4 | 23 |
| β-strand | 68-75 | 8 | 23 |
| α-helix | 89-96 | 8 | |
| α-helix | 108-115 | 8 | |
| β-strand | 119-121 | 3 | 23 |
| β-strand | 124 | 1 | 23 |
| β-strand | 129-136 | 8 | 23 |
| α-helix | 137-139 | 3 | |
| α-helix | 140-151 | 12 | |
| α-helix | 158-174 | 17 | |
| α-helix | 179-191 | 13 | |
| α-helix | 205-208 | 4 | |
| α-helix | 213-223 | 11 | |
| α-helix | 226-228 | 3 | |
| β-strand | 229-232 | 4 | 23 |
| α-helix | 239-248 | 10 | |
| α-helix | 268-270 | 3 | |
| β-strand | 274 | 1 | 24 |
| β-strand | 277-278 | 2 | 24 |
| β-strand | 285-293 | 9 | 24 |
| α-helix | 301-311 | 11 | |
| β-strand | 313-315 | 3 | 24 |
| α-helix | 321-323 | 3 | |
| α-helix | 327-335 | 9 | |
| β-strand | 338-348 | 11 | 24 |
| β-strand | 351-360 | 10 | 24 |
| α-helix | 365-381 | 17 | |
| α-helix | 385-402 | 18 | |
| α-helix | 406-419 | 14 | |
| α-helix | 426-433 | 8 | |
| α-helix | 438-448 | 11 | |
| α-helix | 452-454 | 3 | |
| β-strand | 455-460 | 6 | 24 |
| α-helix | 466-467 | 2 | |
| α-helix | 468-475 | 8 | |
Chain 3B: 21 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| β-strand | 42 | 1 | 32 |
| β-strand | 48-52 | 5 | 32 |
| β-strand | 58-65 | 8 | 32 |
| α-helix | 79-85 | 7 | |
| α-helix | 86-88 | 3 | |
| β-strand | 91 | 1 | 33 |
| β-strand | 94 | 1 | 33 |
| α-helix | 96-106 | 11 | |
| β-strand | 109-114 | 6 | 32 |
| β-strand | 119-126 | 8 | 32 |
| α-helix | 130-142 | 13 | |
| β-strand | 144 | 1 | 33 |
| α-helix | 148-165 | 18 | |
| α-helix | 169-181 | 13 | |
| β-strand | 182 | 1 | 34 |
| α-helix | 202-212 | 11 | |
| α-helix | 215-217 | 3 | |
| β-strand | 219-223 | 5 | 32 |
| α-helix | 227-237 | 11 | |
| α-helix | 246-251 | 6 | |
| β-strand | 253 | 1 | 34 |
| β-strand | 256-257 | 2 | 35 |
| β-strand | 260 | 1 | 35 |
| β-strand | 266-275 | 10 | 35 |
| α-helix | 276-277 | 2 | |
| α-helix | 281-292 | 12 | |
| α-helix | 308-314 | 7 | |
| β-strand | 322-329 | 8 | 35 |
| β-strand | 334-343 | 10 | 35 |
| α-helix | 347-363 | 17 | |
| α-helix | 368-387 | 20 | |
| α-helix | 389-398 | 10 | |
| α-helix | 399-403 | 5 | |
| α-helix | 409-418 | 10 | |
| α-helix | 421-433 | 13 | |
| β-strand | 436-441 | 6 | 35 |
| α-helix | 447-449 | 3 | |
102 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 | 3, 3a | protein | 115 | Mus musculus | P03899 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial | S3, s3 | protein | 263 | Mus musculus | Q9DCT2 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | S2, s2 | protein | 463 | Mus musculus | Q91WD5 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 1 | 1, 1a | protein | 318 | Mus musculus | Q4JFN6 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 6 | 6, 6a | protein | 172 | Mus musculus | P03925 |
| NADH-ubiquinone oxidoreductase chain 4L | 4L, 4l | protein | 98 | Mus musculus | P03903 |
| NADH-ubiquinone oxidoreductase chain 5 | 5, 5a | protein | 607 | Mus musculus | P03921 |
| NADH-ubiquinone oxidoreductase chain 4 | 4, 4a | protein | 459 | Mus musculus | P03911 |
| NADH-ubiquinone oxidoreductase chain 2 | 2, 2a | protein | 345 | Mus musculus | P03893 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | AL, al | protein | 355 | Mus musculus | Q99LC3 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | A9, a9 | protein | 377 | Mus musculus | Q9DC69 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | S4, s4 | protein | 175 | Mus musculus | Q9CXZ1 |
43 more molecules are not listed.
Sequence of entity 1 (3, 3a), FASTA
>8UCA_1 NADH-ubiquinone oxidoreductase chain 3 (chains 3, 3a)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE
Sequence of entity 2 (S3, s3), FASTA
>8UCA_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains S3, s3)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 3 (S2, s2), FASTA
>8UCA_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains S2, s2)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR
Sequence of entity 4 (1, 1a), FASTA
>8UCA_4 NADH-ubiquinone oxidoreductase chain 1 (chains 1, 1a)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM
Sequence of entity 5 (6, 6a), FASTA
>8UCA_5 NADH-ubiquinone oxidoreductase chain 6 (chains 6, 6a)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVINLDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD
Sequence of entity 6 (4L, 4l), FASTA
>8UCA_6 NADH-ubiquinone oxidoreductase chain 4L (chains 4L, 4l)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC
Sequence of entity 7 (5, 5a), FASTA
>8UCA_7 NADH-ubiquinone oxidoreductase chain 5 (chains 5, 5a)
MNIFTTSILLIFILLLSPILISMSNLIKHINFPLYTTTSIKFSFIISLLPLLMFFHNNME
YMITTWHWVTMNSMELKMSFKTDFFSILFTSVALFVTWSIMQFSSWYMHSDPNINRFIKY
LTLFLITMLILTSANNMFQLFIGWEGVGIMSFLLIGWWYGRTDANTAALQAILYNRIGDI
GFILAMVWFSLNMNSWELQQIMFSNNNDNLIPLMGLLIAATGKSAQFGLHPWLPSAMEGP
TPVSALLHSSTMVVAGIFLLVRFHPLTTNNNFILTTMLCLGALTTLFTAICALTQNDIKK
IIAFSTSSQLGLMMVTLGMNQPHLAFLHICTHAFFKAMLFMCSGSIIHSLADEQDIRKMG
NITKIMPFTSSCLVIGSLALTGMPFLTGFYSKDLIIEAINTCNTNAWALLITLIATSMTA
MYSMRIIYFVTMTKPRFPPLISINENDPDLMNPIKRLAFGSIFAGFVISYNIPPTSIPVL
TMPWFLKTTALIISVLGFLIALELNNLTMKLSMNKANPYSSFSTLLGFFPSIIHRITPMK
SLNLSLKTSLTLLDLIWLEKTIPKSTSTLHTNMTTLTTNQKGLIKLYFMSFLINIILIII
LYSINLE
Sequence of entity 8 (4, 4a), FASTA
>8UCA_8 NADH-ubiquinone oxidoreductase chain 4 (chains 4, 4a)
MLKIILPSLMLLPLTWLSSPKKTWTNVTSYSFLISLTSLTLLWQTDENYKNFSNMFSSDP
LSTPLIILTAWLLPLMLMASQNHLKKDNNVLQKLYISMLISLQILLIMTFSATELIMFYI
LFEATLIPTLIIITRWGNQTERLNAGIYFLFYTLIGSIPLLIALILIQNHVGTLNLMILS
FTTHTLDASWSNNLLWLACMMAFLIKMPLYGVHLWLPKAHVEAPIAGSMILAAILLKLGS
YGMIRISIILDPLTKYMAYPFILLSLWGMIMTSSICLRQTDLKSLIAYSSVSHMALVIAS
IMIQTPWSFMGATMLMIAHGLTSSLLFCLANSNYERIHSRTMIMARGLQMVFPLMATWWL
MASLANLALPPSINLMGELFITMSLFSWSNFTIILMGINIIITGMYSMYMIITTQRGKLT
NHMINLQPSHTRELTLMALHMIPLILLTTSPKLITGLTM
Sequence of entity 9 (2, 2a), FASTA
>8UCA_9 NADH-ubiquinone oxidoreductase chain 2 (chains 2, 2a)
MNPITLAIIYFTIFLGPVITMSSTNLMLMWVGLEFSLLAIIPMLINKKNPRSTEAATKYF
VTQATASMIILLAIVLNYKQLGTWMFQQQTNGLILNMTLMALSMKLGLAPFHFWLPEVTQ
GIPLHMGLILLTWQKIAPLSILIQIYPLLNSTIILMLAITSIFMGAWGGLNQTQMRKIMA
YSSIAHMGWMLAILPYNPSLTLLNLMIYIILTAPMFMALMLNNSMTINSISLLWNKTPAM
LTMISLMLLSLGGLPPLTGFLPKWIIITELMKNNCLIMATLMAMMALLNLFFYTRLIYST
SLTMFPTNNNSKMMTHQTKTKPNLMFSTLAIMSTMTLPLAPQLIT
Sequence of entity 10 (AL, al), FASTA
>8UCA_10 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (chains AL, al)
MALRLLRLVPASAPARGLAAGAQRVGRIHTSVHCKLRYGLLAAILGDKTTKKLHEYSRVI
TVDGNICSGKNKLAKEIAQQLGMKHYPEAGIQYSSTTTGDGRPLDIEFSGSCSLEKFYDD
PKSNDGNSYRLQSWLYASRLLQYADALEHLLSTGQGVVLERSIYSDFVFLEAMYNQGYIR
KQCVDHYNEIKRLTLPEYLPPHAVIYIDVPVPEVQSRIQKKGDPHEMKVTSAYLQDIENA
YKKTFLPKMSEMCEVLVYDSWEAEDPTKVVEDIEYLKYNKGPWLKQDDWTFHYLRMLVQD
KTEVLNYTTIPVYLPEITIGAHQGSRIYNSFRELPGRKYAPGYNAEVGDKWIWLK
Sequence of entity 11 (A9, a9), FASTA
>8UCA_11 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains A9, a9)
MAAAVRFRVVRALPMSRPAITAAATSVFCGSSHRQLHHAVIPHGKGGRSSVSGVVATVFG
ATGFLGRYVVNHLGRMGSQVIIPYRCDVYDIMHLRLMGDLGQLTFLEWDARDKDSIRKAV
QHSNVVINLIGREWETRNFDFEDVFVNIPRAIAQASKEAGVERFIHVSHLNASMKSSSKS
LRSKAVGEKEVRSVFPEAIIIRPSDIFGREDRFLNHFANYRWFLAVPLVSLGFKTVKQPV
YVADVSKGIVNATKDPDAVGKTFAFTGPNRYLLFHLVKYIFGMTHRTFIPYPLPLFVYSW
IGKLFGLSPFEPWTTKDKVERIHISDVMPTDLPGLEDLGVQPTPLELKSIEVLRRHRTYR
WLSSEIEETKPAKTVNY
Sequence of entity 12 (S4, s4), FASTA
>8UCA_12 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains S4, s4)
MAAVSISVSLRQAMLGRRAMATAAVSVCRVPSRLLSTSTWKLADNQTRDTQLITVDEKLD
ITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADP
LSNMVLTFSAKEDAIAFAEKNGWSYDVEEKKVPKPKSKSYGANFSWNKRTRVSTK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEC | Heme C | C34 H36 Fe N4 O4 | 2 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 4 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 12 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 2 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 4 |
| EHZ | ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]prop… | C25 H49 N2 O9 P S | 4 |
| ZN | Zinc ion | Zn | 2 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 2 |
| DGT | 2'-deoxyguanosine-5'-triphosphate | C10 H16 N5 O13 P3 | 2 |
| MG | Magnesium ion | Mg | 2 |
Primary citation
Formation of I 2 +III 2 supercomplex rescues respiratory chain defects. Liang, C., Padavannil, A., Zhang, S. et al. Cell Metab (2025) 37:441-459.e11. DOI 10.1016/j.cmet.2024.11.011 · 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).
Browse structure collections
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