9I4I: Human complex I in mitochondria
High resolution Cryo-EM structure of human complex I in mitochondria. Determined by electron microscopy at 2.63 Å resolution. Released 12 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 2.63 Å
- Organism
- Homo sapiens
- Chains
- 45
- Atoms
- 67,696
- Mol. weight
- 1068.01 kDa
- Ligands
- ZN, FES, NDP, FMN
- Released
- 12 Nov 2025
Explore 9I4I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9I4I contains 464 α-helices and 193 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: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 54 | 1 | 26 |
| α-helix | 62-88 | 27 | |
| α-helix | 89-93 | 5 | |
| β-strand | 98 | 1 | 27 |
| α-helix | 100-102 | 3 | |
| α-helix | 109-112 | 4 | |
| α-helix | 116-124 | 9 | |
| α-helix | 127-128 | 2 | |
| α-helix | 129-163 | 35 | |
Chain b: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-23 | 18 | |
| β-strand | 27 | 1 | 26 |
| α-helix | 43-51 | 9 | |
| α-helix | 57-71 | 15 | |
| α-helix | 72-76 | 5 | |
| α-helix | 77-92 | 16 | |
| β-strand | 97-99 | 3 | 28 |
| α-helix | 100-103 | 4 | |
| β-strand | 109 | 1 | 29 |
Chain c: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-36 | 3 | |
| α-helix | 45-54 | 10 | |
| β-strand | 64 | 1 | 30 |
| α-helix | 65-66 | 2 | |
| β-strand | 76 | 1 | 30 |
| α-helix | 83-85 | 3 | |
| β-strand | 94 | 1 | 31 |
| β-strand | 99 | 1 | 31 |
| α-helix | 109-112 | 4 | |
| α-helix | 126-149 | 24 | |
| β-strand | 152 | 1 | 32 |
| α-helix | 158-160 | 3 | |
| α-helix | 162-166 | 5 | |
Chain C: 26 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 57-59 | 3 | |
| α-helix | 65-68 | 4 | |
| α-helix | 73-83 | 11 | |
| β-strand | 86 | 1 | 9 |
| β-strand | 94 | 1 | 9 |
| α-helix | 95-101 | 7 | |
| α-helix | 104-106 | 3 | |
| β-strand | 107 | 1 | 10 |
| β-strand | 109 | 1 | 10 |
| β-strand | 112-117 | 6 | 11 |
| α-helix | 127-133 | 7 | |
| α-helix | 135-149 | 15 | |
| β-strand | 153-158 | 6 | 11 |
| α-helix | 163-179 | 17 | |
| β-strand | 183 | 1 | 12 |
| α-helix | 186-188 | 3 | |
| β-strand | 193 | 1 | 12 |
| β-strand | 195-199 | 5 | 11 |
| α-helix | 204-207 | 4 | |
| α-helix | 209-217 | 9 | |
| α-helix | 223-225 | 3 | |
| α-helix | 235-237 | 3 | |
| β-strand | 240-244 | 5 | 11 |
| α-helix | 245-255 | 11 | |
| α-helix | 260-263 | 4 | |
| β-strand | 273-280 | 8 | 13 |
| β-strand | 286-291 | 6 | 13 |
| β-strand | 295 | 1 | 14 |
| α-helix | 296-302 | 7 | |
| α-helix | 311-313 | 3 | |
| β-strand | 314-318 | 5 | 13 |
| β-strand | 327-328 | 2 | 13 |
| α-helix | 329-332 | 4 | |
| β-strand | 336 | 1 | 14 |
| α-helix | 339-344 | 6 | |
| β-strand | 353-358 | 6 | 13 |
| α-helix | 363-375 | 13 | |
| α-helix | 383 | 1 | |
| α-helix | 384-388 | 5 | |
| α-helix | 389-401 | 13 | |
| α-helix | 408-420 | 13 | |
| α-helix | 427-456 | 30 | |
Chain d: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 13-15 | 3 | |
| β-strand | 18 | 1 | 29 |
| α-helix | 19-21 | 3 | |
| α-helix | 22-31 | 10 | |
| α-helix | 32-36 | 5 | |
| α-helix | 37-52 | 16 | |
| β-strand | 57 | 1 | 27 |
| α-helix | 62-64 | 3 | |
| β-strand | 72 | 1 | 38 |
| α-helix | 76-111 | 36 | |
| α-helix | 112-114 | 3 | |
| α-helix | 119-137 | 19 | |
| α-helix | 146-169 | 24 | |
Chain D: 8 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-38 | 3 | 5 |
| α-helix | 48-60 | 13 | |
| α-helix | 62-75 | 14 | |
| α-helix | 78-79 | 2 | |
| β-strand | 99-101 | 3 | 17 |
| β-strand | 103 | 1 | 18 |
| β-strand | 109 | 1 | 18 |
| α-helix | 116-120 | 5 | |
| β-strand | 126-132 | 7 | 19 |
| β-strand | 138-146 | 9 | 19 |
| α-helix | 155-159 | 5 | |
| β-strand | 165-167 | 3 | 17 |
| β-strand | 175 | 1 | 20 |
| α-helix | 179-181 | 3 | |
| β-strand | 182-183 | 2 | 19 |
| α-helix | 185-194 | 10 | |
| α-helix | 196-206 | 11 | |
Chain e: 9 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-48 | 3 | |
| β-strand | 56 | 1 | 39 |
| α-helix | 58-61 | 4 | |
| α-helix | 66-69 | 4 | |
| α-helix | 80-89 | 10 | |
| α-helix | 90-102 | 13 | |
| α-helix | 103-107 | 5 | |
| α-helix | 116-131 | 16 | |
| α-helix | 144-146 | 3 | |
| α-helix | 148-150 | 3 | |
Chain E: 11 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 58-76 | 19 | |
| β-strand | 81 | 1 | 20 |
| β-strand | 82 | 1 | 21 |
| β-strand | 85 | 1 | 20 |
| α-helix | 89-97 | 9 | |
| α-helix | 103-106 | 4 | |
| β-strand | 111 | 1 | 21 |
| β-strand | 119-123 | 5 | 20 |
| β-strand | 127 | 1 | 22 |
| α-helix | 131-140 | 10 | |
| α-helix | 142 | 1 | |
| β-strand | 146-150 | 5 | 20 |
| α-helix | 151-156 | 6 | |
| α-helix | 158-160 | 3 | |
| β-strand | 166 | 1 | 22 |
| α-helix | 170-172 | 3 | |
| β-strand | 178-180 | 3 | 20 |
| α-helix | 185-186 | 2 | |
| α-helix | 187-202 | 16 | |
| α-helix | 206-211 | 6 | |
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 dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial | Q | protein | 463 | Homo sapiens | O75306 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 | S | protein | 70 | Homo sapiens | O15239 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 | U | protein | 84 | Homo sapiens | O95167 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | V | protein | 141 | Homo sapiens | Q86Y39 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | W | protein | 144 | Homo sapiens | Q9P0J0 |
| Acyl carrier protein, mitochondrial | H, X | protein | 156 | Homo sapiens | O14561 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | Y | protein | 105 | Homo sapiens | O95178 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | Z | protein | 98 | Homo sapiens | O43676 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | a | protein | 189 | Homo sapiens | O43674 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 | b | protein | 128 | Homo sapiens | O95139 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial | c | protein | 186 | Homo sapiens | O95169 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | d | protein | 172 | Homo sapiens | O96000 |
32 more molecules are not listed.
Sequence of entity 1 (Q), FASTA
>9I4I_1 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains Q)
MAALRALCGFRGVAAQVLRPGAGVRLPIQPSRGVRQWQPDVEWAQQFGGAVMYPSKETAH
WKPPPWNDVDPPKDTIVKNITLNFGPQHPAAHGVLRLVMELSGEMVRKCDPHIGLLHRGT
EKLIEYKTYLQALPYFDRLDYVSMMCNEQAYSLAVEKLLNIRPPPRAQWIRVLFGEITRL
LNHIMAVTTHALDLGAMTPFFWLFEEREKMFEFYERVSGARMHAAYIRPGGVHQDLPLGL
MDDIYQFSKNFSLRLDELEELLTNNRIWRNRTIDIGVVTAEEALNYGFSGVMLRGSGIQW
DLRKTQPYDVYDQVEFDVPVGSRGDCYDRYLCRVEEMRQSLRIIAQCLNKMPPGEIKVDD
AKVSPPKRAEMKTSMESLIHHFKLYTEGYQVPPGATYTAIEAPKGEFGVYLVSDGSSRPY
RCKIKAPGFAHLAGLDKMSKGHMLADVVAIIGTQDIVFGEVDR
Sequence of entity 2 (S), FASTA
>9I4I_2 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (chains S)
MWFEILPGLSVMGVCLLIPGLATAYIHRFTNGGKEKRVAHFGYHWSLMERDRRISGVDRY
YVSKGLENID
Sequence of entity 3 (U), FASTA
>9I4I_3 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (chains U)
MAARVGAFLKNAWDKEPVLVVSFVVGGLAVILPPLSPYFKYSVMINKATPYNYPVPVRDD
GNMPDVPSHPQDPQGPSLEWLKKL
Sequence of entity 4 (V), FASTA
>9I4I_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (chains V)
MAPKVFRQYWDIPDGTDCHRKAYSTTSIASVAGLTAAAYRVTLNPPGTFLEGVAKVGQYT
FTAAAVGAVFGLTTCISAHVREKPDDPLNYFLGGCAGGLTLGARTHNYGIGAAACVYFGI
AASLVKMGRLEGWEVFAKPKV
Sequence of entity 5 (W), FASTA
>9I4I_5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (chains W)
MAASKVKQDMPPPGGYGPIDYKRNLPRRGLSGYSMLAIGIGTLIYGHWSIMKWNRERRRL
QIEDFEARIALLPLLQAETDRRTLQMLRENLEEEAIIMKDVPDWKVGESVFHTTRWVPPL
IGELYGLRTTEEALHASHGFMWYT
Sequence of entity 6 (H, X), FASTA
>9I4I_6 Acyl carrier protein, mitochondrial (chains H, X)
MASRVLSAYVSRLPAAFAPLPRVRMLAVARPLSTALCSAGTQTRLGTLQPALVLAQVPGR
VTQLCRQYSDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 7 (Y), FASTA
>9I4I_7 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial (chains Y)
MSALTRLASFARVGGRLFRSGCARTAGDGGVRHAGGGVHIEPRYRQFPQLTRSQVFQSEF
FSGLMWFWILWRFWHDSEEVLGHFPYPDPSQWTDEELGIPPDDED
Sequence of entity 8 (Z), FASTA
>9I4I_8 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (chains Z)
MAHEHGHEHGHHKMELPDYRQWKIEGTPLETIQKKLAAKGLRDPWGRNEAWRYMGGFAKS
VSFSDVFFKGFKWGFAAFVVAVGAEYYLESLNKDKKHH
Sequence of entity 9 (a), FASTA
>9I4I_9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial (chains a)
MAAMSLLRRVSVTAVAALSGRPLGTRLGFGGFLTRGFPKAAAPVRHSGDHGKRLFVIRPS
RFYDRRFLKLLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYVPEHWEYYKHPISRW
IARNFYDSPEKIYERTMAVLQIEAEKAELRVKELEVRKLMHVRGDGPWYYYETIDKELID
HSPKATPDN
Sequence of entity 10 (b), FASTA
>9I4I_10 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (chains b)
MTGYTPDEKLRLQQLRELRRRWLKDQELSPREPVLPPQKMGPMEKFWNKFLENKSPWRKM
VHGVYKKSIFVFTHVLVPVWIIHYYMKYHVSEKPYGIVEKKSRIFPGDTILETGEVIPPM
KEFPDQHH
Sequence of entity 11 (c), FASTA
>9I4I_11 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (chains c)
MAVARAGVLGVQWLQRASRNVMPLGARTASHMTKDMFPGPYPRTPEERAAAAKKYNMRVE
DYEPYPDDGMGYGDYPKLPDRSQHERDPWYSWDQPGLRLNWGEPMHWHLDMYNRNRVDTS
PTPVSWHVMCMQLFGFLAFMIFMCWVGDVYPVYQPVGPKQYPYNNLYLERGGDPSKEPER
VVHYEI
Sequence of entity 12 (d), FASTA
>9I4I_12 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (chains d)
MPDSWDKDVYPEPPRRTPVQPNPIVYMMKAFDLIVDRPVTLVREFIERQHAKNRYYYYHR
QYRRVPDITECKEEDIMCMYEAEMQWKRDYKVDQEIINIMQDRLKACQQREGQNYQQNCI
KEVEQFTQVAKAYQDRYQDLGAYSSARKCLAKQRQRMLQERKAAKEAAAATS
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| MG | Magnesium ion | Mg | 1 |
| DGT | 2'-deoxyguanosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
| PLX | (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2L… | C42 H89 N O8 P | 7 |
| 8Q1 | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C23 H45 N2 O8 P S | 2 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 6 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 7 |
Primary citation
Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome. Nguyen, M.D., Singh, V., Rorbach, J. To be published.
Other PDB entries of the same protein (UniProt O75306 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9TI4 2.66 Å, High resolution Cryo-EM structure of human complex I in mitochondria
- 5XTB 3.4 Å, Cryo-EM structure of human respiratory complex I matrix arm
- 9CWT 3.44 Å, Human kidney respiratory complex I
- 5XTC 3.7 Å, Cryo-EM structure of human respiratory complex I transmembrane arm
- 5XTD 3.7 Å, Cryo-EM structure of human respiratory complex I
- 5XTH 3.9 Å, Cryo-EM structure of human respiratory supercomplex I1III2IV1
- 5XTI 17.4 Å, Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2
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