5XTD: Human respiratory complex I
Cryo-EM structure of human respiratory complex I. Determined by electron microscopy at 3.7 Å resolution. Released 30 Aug 2017.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Homo sapiens
- Chains
- 45
- Atoms
- 66,789
- Mol. weight
- 963.99 kDa
- Ligands
- SF4, FMN, PLX, 8Q1
- Released
- 30 Aug 2017
Explore 5XTD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5XTD contains 468 α-helices and 181 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: 9 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 62-77 | 16 | |
| α-helix | 80-91 | 12 | |
| β-strand | 98 | 1 | 72 |
| 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 | |
| α-helix | 172-175 | 4 | |
| α-helix | 176-178 | 3 | |
Chain A: 23 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 53-58 | 6 | |
| α-helix | 75-81 | 7 | |
| α-helix | 95-100 | 6 | |
| α-helix | 101-103 | 3 | |
| β-strand | 114-116 | 3 | 1 |
| α-helix | 126-133 | 8 | |
| α-helix | 135-149 | 15 | |
| β-strand | 153-158 | 6 | 1 |
| α-helix | 164-178 | 15 | |
| β-strand | 183 | 1 | 2 |
| β-strand | 193 | 1 | 2 |
| β-strand | 194-199 | 6 | 1 |
| α-helix | 204-207 | 4 | |
| α-helix | 209-216 | 8 | |
| α-helix | 223-225 | 3 | |
| α-helix | 235-237 | 3 | |
| β-strand | 242-244 | 3 | 1 |
| α-helix | 245-256 | 12 | |
| α-helix | 259-263 | 5 | |
| β-strand | 273-280 | 8 | 3 |
| β-strand | 286-291 | 6 | 3 |
| β-strand | 295 | 1 | 4 |
| α-helix | 296-301 | 6 | |
| α-helix | 311-313 | 3 | |
| β-strand | 314-319 | 6 | 3 |
| α-helix | 325-326 | 2 | |
| β-strand | 327-328 | 2 | 3 |
| α-helix | 329-332 | 4 | |
| β-strand | 336 | 1 | 4 |
| α-helix | 339-344 | 6 | |
| α-helix | 350-352 | 3 | |
| β-strand | 353-358 | 6 | 3 |
| α-helix | 364-376 | 13 | |
| α-helix | 383-401 | 19 | |
| α-helix | 408-419 | 12 | |
| α-helix | 427-454 | 28 | |
Chain b: 7 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-25 | 20 | |
| α-helix | 41-47 | 7 | |
| α-helix | 49-52 | 4 | |
| α-helix | 56-71 | 16 | |
| α-helix | 72-76 | 5 | |
| α-helix | 77-92 | 16 | |
| β-strand | 97-99 | 3 | 31 |
| α-helix | 122-124 | 3 | |
Chain B: 10 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 36-38 | 3 | 7 |
| α-helix | 42-45 | 4 | |
| α-helix | 48-60 | 13 | |
| α-helix | 63-76 | 14 | |
| α-helix | 78-79 | 2 | |
| β-strand | 99-101 | 3 | 8 |
| β-strand | 103 | 1 | 9 |
| β-strand | 109 | 1 | 9 |
| α-helix | 117-120 | 4 | |
| β-strand | 127 | 1 | 10 |
| β-strand | 130-132 | 3 | 11 |
| β-strand | 138-140 | 3 | 11 |
| β-strand | 144-146 | 3 | 10 |
| α-helix | 155-159 | 5 | |
| β-strand | 165-167 | 3 | 8 |
| β-strand | 175 | 1 | 12 |
| α-helix | 178-181 | 4 | |
| β-strand | 182-184 | 3 | 10 |
| α-helix | 185-194 | 10 | |
| α-helix | 196-206 | 11 | |
| α-helix | 207-209 | 3 | |
Chain c: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| β-strand | 64 | 1 | 5 |
| α-helix | 65-67 | 3 | |
| β-strand | 76 | 1 | 5 |
| α-helix | 83-85 | 3 | |
| α-helix | 103-106 | 4 | |
| α-helix | 110-112 | 3 | |
| α-helix | 126-149 | 24 | |
| β-strand | 152 | 1 | 6 |
| α-helix | 162-166 | 5 | |
| α-helix | 167-169 | 3 | |
Chain C: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 60-76 | 17 | |
| α-helix | 81 | 1 | |
| β-strand | 82 | 1 | 14 |
| α-helix | 83 | 1 | |
| α-helix | 90-96 | 7 | |
| α-helix | 103-106 | 4 | |
| β-strand | 111 | 1 | 14 |
| β-strand | 120-121 | 2 | 15 |
| β-strand | 127 | 1 | 16 |
| α-helix | 131-140 | 10 | |
| α-helix | 142 | 1 | |
| β-strand | 147-148 | 2 | 15 |
| α-helix | 151-156 | 6 | |
| α-helix | 158-160 | 3 | |
| β-strand | 166 | 1 | 16 |
| α-helix | 170-172 | 3 | |
| β-strand | 178 | 1 | 15 |
| β-strand | 179 | 1 | 12 |
| α-helix | 185-186 | 2 | |
| α-helix | 187-202 | 16 | |
| α-helix | 206-211 | 6 | |
Chain d: 10 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| α-helix | 13-15 | 3 | |
| α-helix | 18-21 | 4 | |
| α-helix | 22-31 | 10 | |
| α-helix | 32-36 | 5 | |
| α-helix | 37-52 | 16 | |
| β-strand | 57 | 1 | 72 |
| α-helix | 68-70 | 3 | |
| β-strand | 72 | 1 | 13 |
| α-helix | 77-110 | 34 | |
| α-helix | 116-136 | 21 | |
| α-helix | 146-170 | 25 | |
Chain e: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 57-60 | 4 | |
| α-helix | 66-69 | 4 | |
| α-helix | 80-91 | 12 | |
| α-helix | 92-102 | 11 | |
| α-helix | 103-107 | 5 | |
| α-helix | 115-132 | 18 | |
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 | 431 | Homo sapiens | P49821 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial | B | protein | 176 | Homo sapiens | O00217 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial | C | protein | 156 | Homo sapiens | O75251 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 | E | protein | 113 | Homo sapiens | P56556 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 | F | protein | 83 | Homo sapiens | O43678 |
| Acyl carrier protein, mitochondrial | G, X | protein | 85 | Homo sapiens | O14561 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 | H | protein | 112 | Homo sapiens | Q16718 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 | I | protein | 110 | Homo sapiens | O95182 |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial | J | protein | 337 | Homo sapiens | Q16795 |
| NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial | K | protein | 33 | Homo sapiens | P56181 |
| NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial | L | protein | 118 | Homo sapiens | O43181 |
| NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial | M | protein | 687 | Homo sapiens | P28331 |
32 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5XTD_1 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains A)
PKKTSFGSLKDEDRIFTNLYGRHDWRLKGSLSRGDWYKTKEILLKGPDWILGEIKTSGLR
GRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREILRHDPHKLLEGCLVGG
RAMGARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSGYDFDVFVVRGAGAYIC
GEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFG
RERNSGTKLFNISGHVNHPCTVEEEMSVPLKELIEKHAGGVTGGWDNLLAVIPGGSSTPL
IPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCR
EGVDWMNKVMARFVRGDARPAEIDSLWEISKQIEGHTICALGDGAAWPVQGLIRHFRPEL
EERMQRFAQQH
Sequence of entity 2 (B), FASTA
>5XTD_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains B)
TYKYVNMQDPEMDMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPR
FRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCG
FCQEACPVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 3 (C), FASTA
>5XTD_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains C)
SRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQS
DVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVD
IYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR
Sequence of entity 4 (E), FASTA
>5XTD_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (chains E)
FVKPIFSRDMNEAKRRVRELYRAWYREVPNTVHQFQLDITVKMGRDKVREMFMKNAHVTD
PRVVDLLVIKGKIELEETIKVWKQRTHVMRFFHETEAPRPKDFLSKFYVGHDP
Sequence of entity 5 (F), FASTA
>5XTD_5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains F)
LGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQ
ETNVPLNNFSADQVTRALENVLS
Sequence of entity 6 (G, X), FASTA
>5XTD_6 Acyl carrier protein, mitochondrial (chains G, X)
PPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIP
DIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 7 (H), FASTA
>5XTD_7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (chains H)
LKKTTGLVGLAVCNTPHERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPD
VKKLEDQLQGGQLEEVILQAEHELNLARKMREWKLWEPLVEEPPADQWKWPI
Sequence of entity 8 (I), FASTA
>5XTD_8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (chains I)
ATRLIQRLRNWASGHDLQGKLQLRYQEISKRTQPPPKLPVGPSHKLSNNYYCTRDGRRES
VPPSIIMSSQKALVSGKPAESSAVAATEKKAVTPAPPIKRWELSSDQPYL
Sequence of entity 9 (J), FASTA
>5XTD_9 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains J)
LMPHGKGGRSSVSGIVATVFGATGFLGRYVVNHLGRMGSQVIIPYRCDKYDIMHLRPMGD
LGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWETKNFDFEDVFVKIPQAIAQLSKEA
GVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIVKPSDIFGREDRFLNSFAS
MHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKY
IFAVAHRLFLPFPLPLFAYRWVARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLG
IQATPLELKAIEVLRRHRTYRWLSAEIEDVKPAKTVN
Sequence of entity 10 (K), FASTA
>5XTD_10 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (chains K)
LQHHDYSTYTFLDLNLELSKFRMPQPSSGRESP
Sequence of entity 11 (L), FASTA
>5XTD_11 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains L)
KLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWAST
ADPLSNMVLTFSTKEDAVSFAEKNGWSYDIEERKVPKPKSKSYGANFSWNKRTRVSTK
Sequence of entity 12 (M), FASTA
>5XTD_12 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (chains M)
NLIEVFVDGQSVMVEPGTTVLQACEKVGMQIPRFCYHERLSVAGNCRMCLVEIEKAPKVV
AACAMPVMKGWNILTNSEKSKKAREGVMEFLLANHPLDCPICDQGGECDLQDQSMMFGND
RSRFLEGKRAVEDKNIGPLVKTIMTRCIQCTRCIRFASEIAGVDDLGTTGRGNDMQVGTY
IEKMFMSELSGNIIDICPVGALTSKPYAFTARPWETRKTESIDVMDAVGSNIVVSTRTGE
VMRILPRMHEDINEEWISDKTRFAYDGLKRQRLTEPMVRNEKGLLTYTSWEDALSRVAGM
LQSFQGKDVAAIAGGLVDAEALVALKDLLNRVDSDTLCTEEVFPTAGAGTDLRSNYLLNT
TIAGVEEADVVLLVGTNPRFEAPLFNARIRKSWLHNDLKVALIGSPVDLTYTYDHLGDSP
KILQDIASGSHPFSQVLKEAKKPMVVLGSSALQRNDGAAILAAVSSIAQKIRMTSGVTGD
WKVMNILHRIASQVAALDLGYKPGVEAIRKNPPKVLFLLGADGGCITRQDLPKDCFIIYQ
GHHGDVGAPIADVILPGAAYTEKSATYVNTEGRAQQTKVAVTPPGLAREDWKIIRALSEI
AGMTLPYDTLDQVRNRLEEVSPNLVRYDDIEGANYFQQANELSKLVNQQLLADPLVPPQL
TIKDFYMTDSISRASQTMAKCVKAVTE
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| PLX | (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2L… | C42 H89 N O8 P | 9 |
| 8Q1 | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C23 H45 N2 O8 P S | 2 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 5 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 4 |
Primary citation
Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Guo, R., Zong, S., Wu, M. et al. Cell (2017) 170:1247-1257.e12. DOI 10.1016/j.cell.2017.07.050 · PubMed
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
- 9CWT 3.44 Å, Human kidney 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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