9CWT: Human kidney respiratory complex I
Human kidney respiratory complex I. Determined by electron microscopy at 3.44 Å resolution. Released 6 Aug 2025.
- Method
- Electron microscopy
- Resolution
- 3.44 Å
- Organism
- Homo sapiens
- Chains
- 45
- Atoms
- 60,914
- Mol. weight
- 1008.53 kDa
- Ligands
- SF4, NDP, FES, ZMP
- Released
- 6 Aug 2025
Explore 9CWT in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9CWT contains 410 α-helices and 161 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: 11 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53 | 1 | |
| β-strand | 54 | 1 | 54 |
| α-helix | 55-56 | 2 | |
| α-helix | 58-60 | 3 | |
| α-helix | 62-88 | 27 | |
| α-helix | 89-93 | 5 | |
| β-strand | 97 | 1 | 55 |
| α-helix | 99-102 | 4 | |
| α-helix | 109-112 | 4 | |
| α-helix | 116-124 | 9 | |
| α-helix | 127-128 | 2 | |
| α-helix | 129-163 | 35 | |
| α-helix | 172-175 | 4 | |
| β-strand | 184 | 1 | 56 |
| β-strand | 186 | 1 | 56 |
Chain A: 28 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-39 | 3 | |
| α-helix | 53-58 | 6 | |
| α-helix | 65-70 | 6 | |
| α-helix | 73-83 | 11 | |
| β-strand | 86 | 1 | 1 |
| β-strand | 94 | 1 | 1 |
| α-helix | 95-100 | 6 | |
| α-helix | 110-111 | 2 | |
| β-strand | 112-117 | 6 | 2 |
| α-helix | 126-133 | 8 | |
| α-helix | 135-149 | 15 | |
| β-strand | 153-158 | 6 | 2 |
| α-helix | 160-162 | 3 | |
| α-helix | 163-178 | 16 | |
| β-strand | 183 | 1 | 3 |
| α-helix | 186-188 | 3 | |
| β-strand | 193 | 1 | 3 |
| β-strand | 194-199 | 6 | 2 |
| α-helix | 204-207 | 4 | |
| α-helix | 209-216 | 8 | |
| α-helix | 222-225 | 4 | |
| α-helix | 235-237 | 3 | |
| β-strand | 242-244 | 3 | 2 |
| α-helix | 245-256 | 12 | |
| α-helix | 259-264 | 6 | |
| β-strand | 266 | 1 | 4 |
| β-strand | 271 | 1 | 4 |
| β-strand | 273-280 | 8 | 5 |
| β-strand | 282 | 1 | 6 |
| β-strand | 286-291 | 6 | 5 |
| α-helix | 296-298 | 3 | |
| α-helix | 299-303 | 5 | |
| β-strand | 307 | 1 | 6 |
| α-helix | 311-313 | 3 | |
| β-strand | 314-319 | 6 | 5 |
| β-strand | 327-328 | 2 | 5 |
| α-helix | 329-332 | 4 | |
| α-helix | 339-344 | 6 | |
| α-helix | 350-352 | 3 | |
| β-strand | 353-358 | 6 | 5 |
| α-helix | 363-376 | 14 | |
| α-helix | 383-401 | 19 | |
| α-helix | 408-420 | 13 | |
| α-helix | 427-441 | 15 | |
| α-helix | 443-456 | 14 | |
Chain b: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-26 | 21 | |
| β-strand | 27 | 1 | 54 |
| α-helix | 28-29 | 2 | |
| α-helix | 42-53 | 12 | |
| α-helix | 57-71 | 15 | |
| α-helix | 72-76 | 5 | |
| α-helix | 77-85 | 9 | |
| α-helix | 86-90 | 5 | |
| β-strand | 97-98 | 2 | 23 |
| α-helix | 115-118 | 4 | |
| α-helix | 122-124 | 3 | |
Chain B: 9 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-38 | 3 | 10 |
| α-helix | 42-45 | 4 | |
| α-helix | 48-60 | 13 | |
| α-helix | 62-73 | 12 | |
| α-helix | 78-79 | 2 | |
| β-strand | 99-101 | 3 | 11 |
| β-strand | 103 | 1 | 12 |
| β-strand | 109 | 1 | 12 |
| α-helix | 116-120 | 5 | |
| β-strand | 126-132 | 7 | 13 |
| β-strand | 138-146 | 9 | 13 |
| α-helix | 155-159 | 5 | |
| β-strand | 165-167 | 3 | 11 |
| β-strand | 175 | 1 | 14 |
| α-helix | 178-181 | 4 | |
| β-strand | 182-183 | 2 | 13 |
| α-helix | 185-194 | 10 | |
| α-helix | 196-206 | 11 | |
Chain c: 7 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| β-strand | 64 | 1 | 7 |
| α-helix | 65-66 | 2 | |
| β-strand | 76 | 1 | 7 |
| α-helix | 80-82 | 3 | |
| β-strand | 94 | 1 | 8 |
| β-strand | 99 | 1 | 8 |
| α-helix | 104-106 | 3 | |
| α-helix | 128-149 | 22 | |
| β-strand | 151 | 1 | 9 |
| α-helix | 162-166 | 5 | |
| α-helix | 172-173 | 2 | |
Chain C: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-77 | 18 | |
| β-strand | 81-85 | 5 | 14 |
| α-helix | 89-97 | 9 | |
| α-helix | 103-106 | 4 | |
| β-strand | 119-123 | 5 | 14 |
| β-strand | 127 | 1 | 16 |
| α-helix | 131-140 | 10 | |
| α-helix | 142 | 1 | |
| β-strand | 146-150 | 5 | 14 |
| α-helix | 152-156 | 5 | |
| α-helix | 158-160 | 3 | |
| β-strand | 166 | 1 | 16 |
| β-strand | 178-180 | 3 | 14 |
| α-helix | 185-186 | 2 | |
| α-helix | 187-203 | 17 | |
| α-helix | 206-212 | 7 | |
Chain d: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 18-21 | 4 | |
| α-helix | 22-31 | 10 | |
| α-helix | 32-36 | 5 | |
| α-helix | 37-52 | 16 | |
| β-strand | 56 | 1 | 55 |
| α-helix | 68-70 | 3 | |
| β-strand | 72 | 1 | 15 |
| α-helix | 76-110 | 35 | |
| α-helix | 112-114 | 3 | |
| α-helix | 120-136 | 17 | |
| α-helix | 146-165 | 20 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1-20 | 20 | |
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] flavoprotein 1, mitochondrial | A | protein | 464 | Homo sapiens | P49821 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | B | protein | 210 | Homo sapiens | O00217 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | C | protein | 213 | Homo sapiens | O75251 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | E | protein | 128 | Homo sapiens | P56556 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | F | protein | 99 | Homo sapiens | O43678 |
| Acyl carrier protein, mitochondrial | G, X | protein | 156 | Homo sapiens | O14561 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | H | protein | 116 | Homo sapiens | Q16718 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | I | protein | 113 | Homo sapiens | O95182 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | J | protein | 377 | Homo sapiens | Q16795 |
| NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | K | protein | 108 | Homo sapiens | P56181 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | L | protein | 175 | Homo sapiens | O43181 |
| NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial | M | protein | 727 | Homo sapiens | P28331 |
32 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>9CWT_1 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains A)
MLATRRLLGWSLPARVSVRFSGDTTAPKKTSFGSLKDEDRIFTNLYGRHDWRLKGSLSRG
DWYKTKEILLKGPDWILGEIKTSGLRGRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEG
EPGTCKDREILRHDPHKLLEGCLVGGRAMGARAAYIYIRGEFYNEASNLQVAIREAYEAG
LIGKNACGSGYDFDVFVVRGAGAYICGEETALIESIEGKQGKPRLKPPFPADVGVFGCPT
TVANVETVAVSPTICRRGGTWFAGFGRERNSGTKLFNISGHVNHPCTVEEEMSVPLKELI
EKHAGGVTGGWDNLLAVIPGGSSTPLIPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRS
TDIVKAIARLIEFYKHESCGQCTPCREGVDWMNKVMARFVRGDARPAEIDSLWEISKQIE
GHTICALGDGAAWPVQGLIRHFRPELEERMQRFAQQHQARQAAS
Sequence of entity 2 (B), FASTA
>9CWT_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains B)
MRCLTTPMLLRALAQAARAGPPGGRSLHSSAVAATYKYVNMQDPEMDMKSVTDRAARTLL
WTELFRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHALRRYPSGEERCIACKLCEAI
CPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETHEE
LLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 3 (C), FASTA
>9CWT_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains C)
MAVLSAPGLRGFRILGLRSSVGPAVQARGVHQSVATDGPSSTQPALPKARAVAPKPSSRG
EYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVM
IVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVDIYI
PGCPPTAEALLYGILQLQRKIKRERRLQIWYRR
Sequence of entity 4 (E), FASTA
>9CWT_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (chains E)
MAGSGVRQATSTASTFVKPIFSRDMNEAKRRVRELYRAWYREVPNTVHQFQLDITVKMGR
DKVREMFMKNAHVTDPRVVDLLVIKGKIELEETIKVWKQRTHVMRFFHETEAPRPKDFLS
KFYVGHDP
Sequence of entity 5 (F), FASTA
>9CWT_5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains F)
MAAAAASRGVGAKLGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSD
VQPKLWARYAFGQETNVPLNNFSADQVTRALENVLSGKA
Sequence of entity 6 (G, X), FASTA
>9CWT_6 Acyl carrier protein, mitochondrial (chains G, X)
MASRVLSAYVSRLPAAFAPLPRVRMLAVARPLSTALCSAGTQTRLGTLQPALVLAQVPGR
VTQLCRQYSDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIM
AMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 7 (H), FASTA
>9CWT_7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (chains H)
MAGVLKKTTGLVGLAVCNTPHERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVK
AEPDVKKLEDQLQGGQLEEVILQAEHELNLARKMREWKLWEPLVEEPPADQWKWPI
Sequence of entity 8 (I), FASTA
>9CWT_8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (chains I)
MASATRLIQRLRNWASGHDLQGKLQLRYQEISKRTQPPPKLPVGPSHKLSNNYYCTRDGR
RESVPPSIIMSSQKALVSGKPAESSAVAATEKKAVTPAPPIKRWELSSDQPYL
Sequence of entity 9 (J), FASTA
>9CWT_9 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains J)
MAAAAQSRVVRVLSMSRSAITAIATSVCHGPPCRQLHHALMPHGKGGRSSVSGIVATVFG
ATGFLGRYVVNHLGRMGSQVIIPYRCDKYDIMHLRPMGDLGQLLFLEWDARDKDSIRRVV
QHSNVVINLIGRDWETKNFDFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSRY
LRNKAVGEKVVRDAFPEAIIVKPSDIFGREDRFLNSFASMHRFGPIPLGSLGWKTVKQPV
YVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKYIFAVAHRLFLPFPLPLFAYRW
VARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLGIQATPLELKAIEVLRRHRTYR
WLSAEIEDVKPAKTVNI
Sequence of entity 10 (K), FASTA
>9CWT_10 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (chains K)
MAAPCLLRQGRAGALKTMLQEAQVFRGLASTVSLSAESGKSEKGQPQNSKKQSPPKKPAP
VPAEPFDNTTYKNLQHHDYSTYTFLDLNLELSKFRMPQPSSGRESPRH
Sequence of entity 11 (L), FASTA
>9CWT_11 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains L)
MAAVSMSVVLRQTLWRRRAVAVAALSVSRVPTRSLRTSTWRLAQDQTQDTQLITVDEKLD
ITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWASTADP
LSNMVLTFSTKEDAVSFAEKNGWSYDIEERKVPKPKSKSYGANFSWNKRTRVSTK
Sequence of entity 12 (M), FASTA
>9CWT_12 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains M)
MLRIPVRKALVGLSKSPKGCVRTTATAASNLIEVFVDGQSVMVEPGTTVLQACEKVGMQI
PRFCYHERLSVAGNCRMCLVEIEKAPKVVAACAMPVMKGWNILTNSEKSKKAREGVMEFL
LANHPLDCPICDQGGECDLQDQSMMFGNDRSRFLEGKRAVEDKNIGPLVKTIMTRCIQCT
RCIRFASEIAGVDDLGTTGRGNDMQVGTYIEKMFMSELSGNIIDICPVGALTSKPYAFTA
RPWETRKTESIDVMDAVGSNIVVSTRTGEVMRILPRMHEDINEEWISDKTRFAYDGLKRQ
RLTEPMVRNEKGLLTYTSWEDALSRVAGMLQSFQGKDVAAIAGGLVDAEALVALKDLLNR
VDSDTLCTEEVFPTAGAGTDLRSNYLLNTTIAGVEEADVVLLVGTNPRFEAPLFNARIRK
SWLHNDLKVALIGSPVDLTYTYDHLGDSPKILQDIASGSHPFSQVLKEAKKPMVVLGSSA
LQRNDGAAILAAVSSIAQKIRMTSGVTGDWKVMNILHRIASQVAALDLGYKPGVEAIRKN
PPKVLFLLGADGGCITRQDLPKDCFIIYQGHHGDVGAPIADVILPGAAYTEKSATYVNTE
GRAQQTKVAVTPPGLAREDWKIIRALSEIAGMTLPYDTLDQVRNRLEEVSPNLVRYDDIE
GANYFQQANELSKLVNQQLLADPLVPPQLTIKDFYMTDSISRASQTMAKCVKAVTEGAQA
VEEPSIC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| ZMP | S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C25 H49 N2 O8 P S | 1 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
Primary citation
Human kidney respiratory complex I. Zhang, Z., Lyu, M. To be published.
Other PDB entries of the same protein (UniProt P49821 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9I4I 2.63 Å, High resolution Cryo-EM structure of human complex I in mitochondria
- 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
- 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
Browse structure collections
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