5XTH: Human respiratory supercomplex I1III2IV1
Cryo-EM structure of human respiratory supercomplex I1III2IV1. Determined by electron microscopy at 3.9 Å resolution. Released 13 Sept 2017.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Homo sapiens, Bos taurus
- Chains
- 80
- Atoms
- 115,642
- Mol. weight
- 1662.81 kDa
- Ligands
- HEM, HEC, ZN, HEA
- Released
- 13 Sept 2017
Explore 5XTH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5XTH contains 813 α-helices and 329 β-strands across 80 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 0: 10 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-12 | 5 | |
| β-strand | 19 | 1 | 113 |
| β-strand | 22 | 1 | 113 |
| α-helix | 35-44 | 10 | |
| α-helix | 48-50 | 3 | |
| α-helix | 53-63 | 11 | |
| α-helix | 68-71 | 4 | |
| α-helix | 77-102 | 26 | |
| α-helix | 106-108 | 3 | |
| α-helix | 109-111 | 3 | |
| α-helix | 113-125 | 13 | |
| α-helix | 135-137 | 3 | |
| β-strand | 138-139 | 2 | 114 |
| β-strand | 144-145 | 2 | 114 |
Chain 1: 8 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-20 | 13 | |
| α-helix | 26-36 | 11 | |
| β-strand | 41 | 1 | 115 |
| α-helix | 42-44 | 3 | |
| α-helix | 45-57 | 13 | |
| α-helix | 61-74 | 14 | |
| α-helix | 81-96 | 16 | |
| α-helix | 98-100 | 3 | |
| α-helix | 101-104 | 4 | |
Chain 2: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| α-helix | 15-25 | 11 | |
| α-helix | 35-36 | 2 | |
| β-strand | 37 | 1 | 103 |
| α-helix | 38 | 1 | |
| β-strand | 47-51 | 5 | 117 |
| β-strand | 55-60 | 6 | 102 |
| α-helix | 69 | 1 | |
| β-strand | 70-75 | 6 | 102 |
| β-strand | 80-82 | 3 | 117 |
| β-strand | 86-93 | 8 | 117 |
Chain 3: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-19 | 7 | |
| α-helix | 20-24 | 5 | |
| α-helix | 25-37 | 13 | |
| α-helix | 45-47 | 3 | |
Chain 4: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| β-strand | 24 | 1 | 108 |
| α-helix | 26-44 | 19 | |
| α-helix | 54-63 | 10 | |
| α-helix | 66-78 | 13 | |
Chain 5: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-6 | 4 | |
| β-strand | 10 | 1 | 115 |
| α-helix | 12-35 | 24 | |
| α-helix | 36-41 | 6 | |
| α-helix | 42-50 | 9 | |
| α-helix | 51-53 | 3 | |
| α-helix | 56-65 | 10 | |
Chain 6: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-13 | 9 | |
| α-helix | 26-54 | 29 | |
Chain 7: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-35 | 27 | |
| α-helix | 50-52 | 3 | |
72 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 |
56 more molecules are not listed.
Sequence of entity 1 (A), FASTA
>5XTH_1 NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (chains A)
PKKTSFGSLKDEDRIFTNLYGRHDWRLKGSLSRGDWYKTKEILLKGPDWILGEIKTSGLR
GRGGAGFPTGLKWSFMNKPSDGRPKYLVVNADEGEPGTCKDREILRHDPHKLLEGCLVGG
RAMGARAAYIYIRGEFYNEASNLQVAIREAYEAGLIGKNACGSGYDFDVFVVRGAGAYIC
GEETALIESIEGKQGKPRLKPPFPADVGVFGCPTTVANVETVAVSPTICRRGGTWFAGFG
RERNSGTKLFNISGHVNHPCTVEEEMSVPLKELIEKHAGGVTGGWDNLLAVIPGGSSTPL
IPKSVCETVLMDFDALVQAQTGLGTAAVIVMDRSTDIVKAIARLIEFYKHESCGQCTPCR
EGVDWMNKVMARFVRGDARPAEIDSLWEISKQIEGHTICALGDGAAWPVQGLIRHFRPEL
EERMQRFAQQH
Sequence of entity 2 (B), FASTA
>5XTH_2 NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (chains B)
TYKYVNMQDPEMDMKSVTDRAARTLLWTELFRGLGMTLSYLFREPATINYPFEKGPLSPR
FRGEHALRRYPSGEERCIACKLCEAICPAQAITIEAEPRADGSRRTTRYDIDMTKCIYCG
FCQEACPVDAIVEGPNFEFSTETHEELLYNKEKLLNNGDKWEAEIAANIQADYLYR
Sequence of entity 3 (C), FASTA
>5XTH_3 NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (chains C)
SRGEYVVAKLDDLVNWARRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQS
DVMIVAGTLTNKMAPALRKVYDQMPEPRYVVSMGSCANGGGYYHYSYSVVRGCDRIVPVD
IYIPGCPPTAEALLYGILQLQRKIKRERRLQIWYRR
Sequence of entity 4 (E), FASTA
>5XTH_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (chains E)
FVKPIFSRDMNEAKRRVRELYRAWYREVPNTVHQFQLDITVKMGRDKVREMFMKNAHVTD
PRVVDLLVIKGKIELEETIKVWKQRTHVMRFFHETEAPRPKDFLSKFYVGHDP
Sequence of entity 5 (F), FASTA
>5XTH_5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (chains F)
LGLREIRIHLCQRSPGSQGVRDFIEKRYVELKKANPDLPILIRECSDVQPKLWARYAFGQ
ETNVPLNNFSADQVTRALENVLS
Sequence of entity 6 (G, X), FASTA
>5XTH_6 Acyl carrier protein, mitochondrial (chains G, X)
PPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIP
DIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 7 (H), FASTA
>5XTH_7 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 (chains H)
LKKTTGLVGLAVCNTPHERLRILYTKILDVLEEIPKNAAYRKYTEQITNEKLAMVKAEPD
VKKLEDQLQGGQLEEVILQAEHELNLARKMREWKLWEPLVEEPPADQWKWPI
Sequence of entity 8 (I), FASTA
>5XTH_8 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (chains I)
ATRLIQRLRNWASGHDLQGKLQLRYQEISKRTQPPPKLPVGPSHKLSNNYYCTRDGRRES
VPPSIIMSSQKALVSGKPAESSAVAATEKKAVTPAPPIKRWELSSDQPYL
Sequence of entity 9 (J), FASTA
>5XTH_9 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial (chains J)
LMPHGKGGRSSVSGIVATVFGATGFLGRYVVNHLGRMGSQVIIPYRCDKYDIMHLRPMGD
LGQLLFLEWDARDKDSIRRVVQHSNVVINLIGRDWETKNFDFEDVFVKIPQAIAQLSKEA
GVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIVKPSDIFGREDRFLNSFAS
MHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKY
IFAVAHRLFLPFPLPLFAYRWVARVFEISPFEPWITRDKVERMHITDMKLPHLPGLEDLG
IQATPLELKAIEVLRRHRTYRWLSAEIEDVKPAKTVN
Sequence of entity 10 (K), FASTA
>5XTH_10 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial (chains K)
LQHHDYSTYTFLDLNLELSKFRMPQPSSGRESP
Sequence of entity 11 (L), FASTA
>5XTH_11 NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial (chains L)
KLDITTLTGVPEEHIKTRKVRIFVPARNNMQSGVNNTKKWKMEFDTRERWENPLMGWAST
ADPLSNMVLTFSTKEDAVSFAEKNGWSYDIEERKVPKPKSKSYGANFSWNKRTRVSTK
Sequence of entity 12 (M), FASTA
>5XTH_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 |
|---|
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 4 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 2 |
| ZN | Zinc ion | Zn | 1 |
| HEA | Heme-a | C49 H56 Fe N4 O6 | 2 |
| MG | Magnesium ion | Mg | 1 |
| CU | Copper (II) ion | Cu | 3 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 10 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 14 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 4 |
| NDP | NADPH dihydro-nicotinamide-adenine-dinucleotide phosphate | C21 H30 N7 O17 P3 | 1 |
| 8Q1 | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C23 H45 N2 O8 P S | 2 |
| PLX | (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2L… | C42 H89 N O8 P | 12 |
| FMN | Flavin mononucleotide | C17 H21 N4 O9 P | 1 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 6 |
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
- 5XTD 3.7 Å, Cryo-EM structure of human respiratory complex I
- 5XTI 17.4 Å, Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2
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