8IBF: PDB entry 8IBF
Respiratory complex Membrane domain of CI, focus-refined of type II, Wild type mouse under cold temperature. Determined by electron microscopy at 3.3 Å resolution. Released 18 Sept 2024.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Mus musculus
- Chains
- 24
- Atoms
- 31,948
- Mol. weight
- 567.51 kDa
- Ligands
- EHZ, ADP, CDL, 3PE
- Released
- 18 Sept 2024
Explore 8IBF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8IBF contains 230 α-helices and 44 β-strands across 24 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 c: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-72 | 32 | |
Chain d: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-19 | 4 | |
| α-helix | 22-25 | 4 | |
| α-helix | 29-48 | 20 | |
| α-helix | 58-96 | 39 | |
Chain D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-46 | 6 | |
| α-helix | 58-60 | 3 | |
| α-helix | 63-65 | 3 | |
Chain e: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 24-25 | 2 | |
| α-helix | 26-28 | 3 | |
| α-helix | 34-41 | 8 | |
| α-helix | 49-51 | 3 | |
| α-helix | 55-57 | 3 | |
| α-helix | 58-66 | 9 | |
| α-helix | 70-88 | 19 | |
Chain f: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-33 | 19 | |
| α-helix | 46-49 | 4 | |
Chain g: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 59-62 | 4 | |
| α-helix | 78-85 | 8 | |
| α-helix | 88-89 | 2 | |
| α-helix | 90-97 | 8 | |
| α-helix | 99-105 | 7 | |
| α-helix | 110-112 | 3 | |
| α-helix | 113-130 | 18 | |
Chain h: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 54 | 1 | 13 |
| α-helix | 63-88 | 26 | |
| α-helix | 89-93 | 5 | |
| β-strand | 97-98 | 2 | 14 |
| α-helix | 109-112 | 4 | |
| α-helix | 116-125 | 10 | |
| α-helix | 129-163 | 35 | |
| α-helix | 176-178 | 3 | |
Chain i: 6 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-26 | 16 | |
| β-strand | 27 | 1 | 13 |
| α-helix | 28-29 | 2 | |
| α-helix | 70-85 | 16 | |
| α-helix | 86-90 | 5 | |
| β-strand | 97-99 | 3 | 2 |
| α-helix | 100-103 | 4 | |
| β-strand | 109 | 1 | 15 |
| β-strand | 110 | 1 | 16 |
| β-strand | 116 | 1 | 15 |
| α-helix | 117-122 | 6 | |
16 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 dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | D | protein | 463 | Mus musculus | Q91WD5 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 6 | J | protein | 172 | Mus musculus | P03925 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 4L | K | protein | 98 | Mus musculus | P03903 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 5 | L | protein | 607 | Mus musculus | P03921 (AlphaFold model) |
| NADH-ubiquinone oxidoreductase chain 4 | M | protein | 459 | Mus musculus | P03911 |
| NADH-ubiquinone oxidoreductase chain 2 | N | protein | 345 | Mus musculus | P03893 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial | O | protein | 355 | Mus musculus | Q99LC3 |
| Acyl carrier protein, mitochondrial | U | protein | 156 | Mus musculus | Q9CR21 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 | X | protein | 172 | Mus musculus | Q9DCJ5 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | Y | protein | 143 | Mus musculus | G5E814 |
| NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | c | protein | 76 | Mus musculus | Q9CQY9 |
| NADH dehydrogenase [ubiquinone] 1 subunit C2 | d | protein | 120 | Mus musculus | Q9CQ54 |
12 more molecules are not listed.
Sequence of entity 1 (D), FASTA
>8IBF_1 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains D)
MAALRALRCLRGVGAPVLRPGSGIRLPSQPSRGARQWQPDIEWAEQFSGAVMYPSKETAH
WKPPPWNDVDILKEKAVTNMTLNFGPQHPAAHGVLRLVLELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSIAVEKLLNIQPPPRAQWIRVLFGEITRI
LNHIMAVTTHALDIGAMTPFFWMFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
LDDIYEFSKNFSLRIDEVEEMLTNNRIWRNRTVDIGVVTAEDALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPIGSRGDCYDRYLCRVEEMRQSLRIIEQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEIDR
Sequence of entity 2 (J), FASTA
>8IBF_2 NADH-ubiquinone oxidoreductase chain 6 (chains J)
MNNYIFVLSSLFLVGCLGLALKPSPIYGGLGLIVSGFVGCLMVLGFGGSFLGLMVFLIYL
GGMLVVFGYTTAMATEEYPETWGSNWLILGFLVLGVIMEVFLICVLNYYDEVGVILGDGL
GDWLMYEVDDVGVMLEGGIGVAAMYSCATWMMVVAGWSLFAGIFIIIEITRD
Sequence of entity 3 (K), FASTA
>8IBF_3 NADH-ubiquinone oxidoreductase chain 4L (chains K)
MPSTFFNLTMAFSLSLLGTLMFRSHLMSTLLCLEGMVLSLFIMTSVTSLNSNSMSSMPIP
ITILVFAACEAAVGLALLVKVSNTYGTDYVQNLNLLQC
Sequence of entity 4 (L), FASTA
>8IBF_4 NADH-ubiquinone oxidoreductase chain 5 (chains L)
MNIFTTSILLIFILLLSPILISMSNLIKHINFPLYTTTSIKFSFIISLLPLLMFFHNNME
YMITTWHWVTMNSMELKMSFKTDFFSILFTSVALFVTWSIMQFSSWYMHSDPNINRFIKY
LTLFLITMLILTSANNMFQLFIGWEGVGIMSFLLIGWWYGRTDANTAALQAILYNRIGDI
GFILAMVWFSLNMNSWELQQIMFSNNNDNLIPLMGLLIAATGKSAQFGLHPWLPSAMEGP
TPVSALLHSSTMVVAGIFLLVRFHPLTTNNNFILTTMLCLGALTTLFTAICALTQNDIKK
IIAFSTSSQLGLMMVTLGMNQPHLAFLHICTHAFFKAMLFMCSGSIIHSLADEQDIRKMG
NITKIMPFTSSCLVIGSLALTGMPFLTGFYSKDLIIEAINTCNTNAWALLITLIATSMTA
MYSMRIIYFVTMTKPRFPPLISINENDPDLMNPIKRLAFGSIFAGFVISYNIPPTSIPVL
TMPWFLKTTALIISVLGFLIALELNNLTMKLSMNKANPYSSFSTLLGFFPSIIHRITPMK
SLNLSLKTSLTLLDLIWLEKTIPKSTSTLHTNMTTLTTNQKGLIKLYFMSFLINIILIII
LYSINLE
Sequence of entity 5 (M), FASTA
>8IBF_5 NADH-ubiquinone oxidoreductase chain 4 (chains M)
MLKIILPSLMLLPLTWLSSPKKTWTNVTSYSFLISLTSLTLLWQTDENYKNFSNMFSSDP
LSTPLIILTAWLLPLMLMASQNHLKKDNNVLQKLYISMLISLQILLIMTFSATELIMFYI
LFEATLIPTLIIITRWGNQTERLNAGIYFLFYTLIGSIPLLIALILIQNHVGTLNLMILS
FTTHTLDASWSNNLLWLACMMAFLIKMPLYGVHLWLPKAHVEAPIAGSMILAAILLKLGS
YGMIRISIILDPLTKYMAYPFILLSLWGMIMTSSICLRQTDLKSLIAYSSVSHMALVIAS
IMIQTPWSFMGATMLMIAHGLTSSLLFCLANSNYERIHSRTMIMARGLQMVFPLMATWWL
MASLANLALPPSINLMGELFITMSLFSWSNFTIILMGINIIITGMYSMYMIITTQRGKLT
NHMINLQPSHTRELTLMALHMIPLILLTTSPKLITGLTM
Sequence of entity 6 (N), FASTA
>8IBF_6 NADH-ubiquinone oxidoreductase chain 2 (chains N)
MNPITLAIIYFTIFLGPVITMSSTNLMLMWVGLEFSLLAIIPMLINKKNPRSTEAATKYF
VTQATASMIILLAIVLNYKQLGTWMFQQQTNGLILNMTLMALSMKLGLAPFHFWLPEVTQ
GIPLHMGLILLTWQKIAPLSILIQIYPLLNSTIILMLAITSIFMGAWGGLNQTQMRKIMA
YSSIAHMGWMLAILPYNPSLTLLNLMIYIILTAPMFMALMLNNSMTINSISLLWNKTPAM
LTMISLMLLSLGGLPPLTGFLPKWIIITELMKNNCLIMATLMAMMALLNLFFYTRLIYST
SLTMFPTNNNSKMMTHQTKTKPNLMFSTLAIMSTMTLPLAPQLIT
Sequence of entity 7 (O), FASTA
>8IBF_7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial (chains O)
MALRLLRLVPASAPARGLAAGAQRVGRIHTSVHCKLRYGLLAAILGDKTTKKLHEYSRVI
TVDGNICSGKNKLAKEIAQQLGMKHYPEAGIQYSSTTTGDGRPLDIEFSGSCSLEKFYDD
PKSNDGNSYRLQSWLYASRLLQYADALEHLLSTGQGVVLERSIYSDFVFLEAMYNQGYIR
KQCVDHYNEIKRLTLPEYLPPHAVIYIDVPVPEVQSRIQKKGDPHEMKVTSAYLQDIENA
YKKTFLPKMSEMCEVLVYDSWEAEDPTKVVEDIEYLKYNKGPWLKQDDWTFHYLRMLVQD
KTEVLNYTTIPVYLPEITIGAHQGSRIYNSFRELPGRKYAPGYNAEVGDKWIWLK
Sequence of entity 8 (U), FASTA
>8IBF_8 Acyl carrier protein, mitochondrial (chains U)
MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGT
VTHLCRQYSDAPPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 9 (X), FASTA
>8IBF_9 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 (chains X)
MPGIVELPTLEELKVEEVKVSSAVLKAAAHHYGAQCDKTNKEFMLCRWEEKDPRRCLKEG
KLVNGCALNFFRQIKSHCAEPFTEYWTCLDYSNMQLFRHCRQQQAKFDQCVLDKLGWVRP
DLGQLSKVTKVKTDRPLPENPYHSRARPEPNPVIEGDLKPAKHGTRFFFWTV
Sequence of entity 10 (Y), FASTA
>8IBF_10 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (chains Y)
MAMVKRFFESYHEVPDGTQCHRKTYITTALGGICGIIGSAYSVSLNPADSTLEAVARVGR
YTFTAAAIGAMFGLTTCVSAQVREKPDDPLNYFIGGCAGGLTLGARTHSYGTAAMGCVYM
GTAAALFKIGKLEGWELFPTPKV
Sequence of entity 11 (c), FASTA
>8IBF_11 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial (chains c)
MAPSVVLRSFSRLLAPARLPSCSSTRSKFYVREPVNAKPNWLAVGLSVGASVFMWIYLIQ
THNEDVLEYKRRNGLE
Sequence of entity 12 (d), FASTA
>8IBF_12 NADH dehydrogenase [ubiquinone] 1 subunit C2 (chains d)
MMNGRPGHEPLKFLPDEARSLPPPKLNDPRLVYMGLLGYCTGLMDNMLRMRPVMRAGLHR
QLLFVTSFVFAGYFYLKRQNYLYAVKDHDMFGYIKLHPEDFPEKEKKTYAEILEPFHPVR
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 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 3 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 14 |
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 Q91WD5 (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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