8XNR: NADH-ubiquinone oxidoreductase chain 3
Respiratory complex Peripheral Arm of CI, close form A, focus-refined map of type IB, Wild type mouse under Cold Acclimation. Determined by electron microscopy at 3.3 Å resolution. Released 30 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Mus musculus
- Chains
- 23
- Atoms
- 33,911
- Mol. weight
- 576.64 kDa
- Ligands
- EHZ, ZN, NDP, UQ9
- Released
- 30 Oct 2024
Explore 8XNR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8XNR contains 218 α-helices and 143 β-strands across 23 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
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-30 | 26 | |
| α-helix | 35-37 | 3 | |
| α-helix | 42-54 | 13 | |
Chain A: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
| α-helix | 24-26 | 3 | |
| α-helix | 53-72 | 20 | |
| α-helix | 75-79 | 5 | |
| α-helix | 85-107 | 23 | |
Chain b: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-14 | 8 | |
| α-helix | 19-31 | 13 | |
| α-helix | 39-48 | 10 | |
| α-helix | 55-56 | 2 | |
| β-strand | 57 | 1 | 49 |
| α-helix | 58 | 1 | |
| β-strand | 66-67 | 2 | 49 |
Chain B: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 71-88 | 18 | |
| β-strand | 92-94 | 3 | 1 |
| α-helix | 100-108 | 9 | |
| α-helix | 115-117 | 3 | |
| β-strand | 130-134 | 5 | 1 |
| β-strand | 138 | 1 | 2 |
| α-helix | 142-150 | 9 | |
| β-strand | 157-161 | 5 | 1 |
| α-helix | 163-166 | 4 | |
| α-helix | 169-171 | 3 | |
| β-strand | 177 | 1 | 2 |
| β-strand | 189-191 | 3 | 1 |
| α-helix | 198-214 | 17 | |
| α-helix | 217-222 | 6 | |
Chain C: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 51-67 | 17 | |
| β-strand | 72-78 | 7 | 3 |
| β-strand | 82-87 | 6 | 3 |
| α-helix | 89-91 | 3 | |
| α-helix | 92-100 | 9 | |
| α-helix | 103-105 | 3 | |
| β-strand | 109-117 | 9 | 3 |
| β-strand | 125-133 | 9 | 3 |
| β-strand | 138-143 | 6 | 3 |
| β-strand | 146 | 1 | 3 |
| β-strand | 152-153 | 2 | 4 |
| α-helix | 162-173 | 12 | |
| β-strand | 177-178 | 2 | 4 |
| β-strand | 207-212 | 6 | 5 |
| β-strand | 217-222 | 6 | 5 |
Chain D: 20 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82-83 | 2 | 6 |
| β-strand | 96-102 | 7 | 6 |
| β-strand | 105-112 | 8 | 6 |
| α-helix | 120-125 | 6 | |
| α-helix | 129-131 | 3 | |
| α-helix | 133-137 | 5 | |
| α-helix | 144-158 | 15 | |
| α-helix | 165-194 | 30 | |
| α-helix | 198-217 | 20 | |
| β-strand | 227-228 | 2 | 7 |
| β-strand | 231-232 | 2 | 7 |
| α-helix | 235-237 | 3 | |
| α-helix | 240-262 | 23 | |
| α-helix | 268-272 | 5 | |
| α-helix | 280-285 | 6 | |
| β-strand | 290 | 1 | 8 |
| α-helix | 291-295 | 5 | |
| α-helix | 302-305 | 4 | |
| β-strand | 318-320 | 3 | 9 |
| α-helix | 326-349 | 24 | |
| β-strand | 357 | 1 | 7 |
| α-helix | 365-367 | 3 | |
| α-helix | 368-371 | 4 | |
| α-helix | 375-386 | 12 | |
| α-helix | 391-392 | 2 | |
| β-strand | 394 | 1 | 10 |
| β-strand | 397-401 | 5 | 11 |
| β-strand | 405 | 1 | 8 |
| β-strand | 406-412 | 7 | 11 |
| β-strand | 413 | 1 | 10 |
| β-strand | 421-425 | 5 | 11 |
| α-helix | 429-438 | 10 | |
| β-strand | 442 | 1 | 6 |
| α-helix | 444-452 | 9 | |
| α-helix | 458-462 | 5 | |
Chain E: 11 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 56-68 | 13 | |
| α-helix | 70 | 1 | |
| α-helix | 75-77 | 3 | |
| α-helix | 78-88 | 11 | |
| α-helix | 94-103 | 10 | |
| α-helix | 108-117 | 10 | |
| β-strand | 131-133 | 3 | 12 |
| α-helix | 137-141 | 5 | |
| α-helix | 144-155 | 12 | |
| β-strand | 162 | 1 | 13 |
| β-strand | 169 | 1 | 13 |
| β-strand | 171 | 1 | 12 |
| β-strand | 184-187 | 4 | 12 |
| β-strand | 192-193 | 2 | 12 |
| α-helix | 197-208 | 12 | |
| β-strand | 217 | 1 | 12 |
| α-helix | 236-238 | 3 | |
| α-helix | 244-246 | 3 | |
Chain F: 25 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-59 | 7 | |
| α-helix | 65-71 | 7 | |
| α-helix | 73-83 | 11 | |
| α-helix | 85 | 1 | |
| β-strand | 86 | 1 | 14 |
| α-helix | 87 | 1 | |
| β-strand | 94 | 1 | 14 |
| α-helix | 95-101 | 7 | |
| α-helix | 105-106 | 2 | |
| β-strand | 112-116 | 5 | 15 |
| α-helix | 126-133 | 8 | |
| α-helix | 135-149 | 15 | |
| β-strand | 153-158 | 6 | 15 |
| α-helix | 163-179 | 17 | |
| β-strand | 183 | 1 | 16 |
| α-helix | 186-188 | 3 | |
| β-strand | 193 | 1 | 16 |
| β-strand | 195-199 | 5 | 15 |
| α-helix | 205-207 | 3 | |
| α-helix | 209-217 | 9 | |
| α-helix | 223-225 | 3 | |
| α-helix | 235-237 | 3 | |
| β-strand | 240-244 | 5 | 15 |
| α-helix | 245-265 | 21 | |
| β-strand | 276-279 | 4 | 17 |
| β-strand | 282 | 1 | 18 |
| β-strand | 286-288 | 3 | 17 |
| β-strand | 295 | 1 | 19 |
| α-helix | 296-302 | 7 | |
| α-helix | 306 | 1 | |
| β-strand | 307 | 1 | 18 |
| β-strand | 316-318 | 3 | 17 |
| α-helix | 325-326 | 2 | |
| β-strand | 327 | 1 | 17 |
| α-helix | 329-332 | 4 | |
| β-strand | 336 | 1 | 19 |
| α-helix | 339-344 | 6 | |
| β-strand | 353-357 | 5 | 17 |
| α-helix | 363-375 | 13 | |
| α-helix | 383-401 | 19 | |
| α-helix | 408-422 | 15 | |
| α-helix | 426-456 | 31 | |
15 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 dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | P | protein | 377 | Mus musculus | Q9DC69 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | Q | protein | 175 | Mus musculus | Q9CXZ1 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | R | protein | 116 | Mus musculus | P52503 |
11 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>8XNR_1 NADH-ubiquinone oxidoreductase chain 3 (chains A)
MNLYTVIFINILLSLTLILVAFWLPQMNLYSEKANPYECGFDPTSSARLPFSMKFFLVAI
TFLLFDLEIALLLPLPWAIQTIKTSTMMIMAFILVTILSLGLAYEWTQKGLEWTE
Sequence of entity 2 (B), FASTA
>8XNR_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains B)
MAALAAPGLLSVRILGLRTAQVQLRRVHQSVATEGPSPSPSPSLSSTQSAVSKAGAGAVV
PKLSHLPRSRAEYVVTKLDDLINWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVV
FRASPRQADVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRG
CDRIVPVDIYVPGCPPTAEALLYGILQLQRKIKREQKLKIWYRR
Sequence of entity 3 (C), FASTA
>8XNR_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (chains C)
MAAAAARVWCRGLLGAASVGRGAGRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAF
GEYVAEILPKYVQQVQVSCLDELEICIHPDGVIPTLTFLRDHTNAQFKSLADLTAVDVPT
RQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIVSVHIAANWYEREVWDMFGVFFFNH
PDLRRILTDYGFEGHPFRKDFPLTGYVELRYDDEVKRVVAEPVELAQEFRKFDLNSPWEA
FPAYRQPPESLKLEAGDKKPETK
Sequence of entity 4 (D), FASTA
>8XNR_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
>8XNR_5 NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (chains E)
MFSLALRARATGLAAQWGRHARNLHKTAVHNGAGGALFVHRDTPENNPDTPFDFTPENYK
RIEAIVKNYPEGHQAAAVLPVLDLAQRQNGWLPISAMNKVAEVLQVPPMRVYEVATFYTM
YNRKPVGKYHIQVCTTTPCMLRDSDSILETLQRKLGIKVGETTPDKLFTLIEVECLGACV
NAPMVQINDNYYEDLTPKDIEEIIDELKAGKVPKPGPRSGRFCCEPAGGLTSLTEPPKGP
GFGVQAGL
Sequence of entity 6 (F), FASTA
>8XNR_6 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains F)
MLAARHFLGGLVPVRVSVRFSSGTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGALRRG
DWYKTKEILLKGPDWILGEMKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREIMRHDPHKLVEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSDYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVKGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEDRMQRFAQQHRAWQAAS
Sequence of entity 7 (G), FASTA
>8XNR_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
>8XNR_8 NADH-ubiquinone oxidoreductase chain 1 (chains H)
MFFINILTLLVPILIAMAFLTLVERKILGYMQLRKGPNIVGPYGILQPFADAMKLFMKEP
MRPLTTSMSLFIIAPTLSLTLALSLWVPLPMPHPLINLNLGILFILATSSLSVYSILWSG
WASNSKYSLFGALRAVAQTISYEVTMAIILLSVLLMNGSYSLQTLITTQEHMWLLLPAWP
MAMMWFISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFALFFMAEYTNIILMNALTTI
IFLGPLYYINLPELYSTNFMMEALLLSSTFLWIRASYPRFRYDQLMHLLWKNFLPLTLAL
CMWHISLPIFTAGVPPYM
Sequence of entity 9 (I), FASTA
>8XNR_9 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains I)
MYRLSSSMLPRALAQAMRTGHLNGQSLHSSAVAATYKYVNKKEQESEVDMKSATDNAARI
LMWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCE
AICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH
EELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 10 (P), FASTA
>8XNR_10 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains P)
MAAAVRFRVVRALPMSRPAITAAATSVFCGSSHRQLHHAVIPHGKGGRSSVSGVVATVFG
ATGFLGRYVVNHLGRMGSQVIIPYRCDVYDIMHLRLMGDLGQLTFLEWDARDKDSIRKAV
QHSNVVINLIGREWETRNFDFEDVFVNIPRAIAQASKEAGVERFIHVSHLNASMKSSSKS
LRSKAVGEKEVRSVFPEAIIIRPSDIFGREDRFLNHFANYRWFLAVPLVSLGFKTVKQPV
YVADVSKGIVNATKDPDAVGKTFAFTGPNRYLLFHLVKYIFGMTHRTFIPYPLPLFVYSW
IGKLFGLSPFEPWTTKDKVERIHISDVMPTDLPGLEDLGVQPTPLELKSIEVLRRHRTYR
WLSSEIEETKPAKTVNY
Sequence of entity 11 (Q), FASTA
>8XNR_11 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains Q)
MAAVSISVSLRQAMLGRRAMATAAVSVCRVPSRLLSTSTWKLADNQTRDTQLITVDEKLD
ITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADP
LSNMVLTFSAKEDAIAFAEKNGWSYDVEEKKVPKPKSKSYGANFSWNKRTRVSTK
Sequence of entity 12 (R), FASTA
>8XNR_12 NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial (chains R)
MAAVLTFRRLLTLPRAARGFGVQVSPSGEKITHTGQVYDEKDYRRVRFVDRQKEVNENFA
IDLIAQQPVNEVEHRIIACDGGGGALGHPKVYINLDKETKTGTCGYCGLQFKQHHH
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 | 1 |
| ZN | Zinc ion | Zn | 1 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| UQ9 | Ubiquinone-9 | C54 H82 O4 | 1 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| UQ1 | Ubiquinone-1 | C14 H18 O4 | 1 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 2 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 3 |
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:
- 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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