5XTC: Human respiratory complex I transmembrane arm
Cryo-EM structure of human respiratory complex I transmembrane arm. Determined by electron microscopy at 3.7 Å resolution. Released 30 Aug 2017.
- Method
- Electron microscopy
- Resolution
- 3.7 Å
- Organism
- Homo sapiens
- Chains
- 29
- Atoms
- 38,835
- Mol. weight
- 561.08 kDa
- Ligands
- PLX, CDL, PEE, 8Q1
- Released
- 30 Aug 2017
Explore 5XTC in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5XTC contains 276 α-helices and 44 β-strands across 29 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 | 6 |
| 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 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 | 7 |
| α-helix | 122-124 | 3 | |
Chain c: 8 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-54 | 10 | |
| β-strand | 64 | 1 | 8 |
| α-helix | 65-67 | 3 | |
| β-strand | 76 | 1 | 8 |
| α-helix | 83-85 | 3 | |
| α-helix | 103-106 | 4 | |
| α-helix | 110-112 | 3 | |
| α-helix | 126-149 | 24 | |
| β-strand | 152 | 1 | 9 |
| α-helix | 162-166 | 5 | |
| α-helix | 167-169 | 3 | |
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 | 6 |
| α-helix | 68-70 | 3 | |
| β-strand | 72 | 1 | 10 |
| 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 | |
Chain f: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 34-36 | 3 | |
| α-helix | 42-72 | 31 | |
Chain g: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-19 | 5 | |
| α-helix | 21-24 | 4 | |
| α-helix | 28-47 | 20 | |
| α-helix | 57-95 | 39 | |
| α-helix | 97-99 | 3 | |
| α-helix | 103-106 | 4 | |
| β-strand | 107 | 1 | 10 |
Chain h: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-9 | 4 | |
| α-helix | 16-18 | 3 | |
| α-helix | 26-28 | 3 | |
| α-helix | 35-43 | 9 | |
| α-helix | 52-55 | 4 | |
| α-helix | 57-68 | 12 | |
| α-helix | 70-84 | 15 | |
21 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 | 46 | 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 | 83 | Homo sapiens | O95167 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 | V | protein | 140 | Homo sapiens | Q86Y39 (AlphaFold model) |
| NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 | W | protein | 116 | Homo sapiens | Q9P0J0 |
| Acyl carrier protein, mitochondrial | X | protein | 85 | Homo sapiens | O14561 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial | Y | protein | 59 | Homo sapiens | O95178 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 | Z | protein | 80 | Homo sapiens | O43676 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial | a | protein | 138 | 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 | 153 | Homo sapiens | O95169 |
| NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 | d | protein | 171 | Homo sapiens | O96000 |
17 more molecules are not listed.
Sequence of entity 1 (Q), FASTA
>5XTC_1 NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (chains Q)
VRQWQPDVEWAQQFGGAVMYPSKETAHWKPPPWNDVDPPKDTIVKN
Sequence of entity 2 (S), FASTA
>5XTC_2 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 (chains S)
MWFEILPGLSVMGVCLLIPGLATAYIHRFTNGGKEKRVAHFGYHWSLMERDRRISGVDRY
YVSKGLENID
Sequence of entity 3 (U), FASTA
>5XTC_3 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 (chains U)
AARVGAFLKNAWDKEPVLVVSFVVGGLAVILPPLSPYFKYSVMINKATPYNYPVPVRDDG
NMPDVPSHPQDPQGPSLEWLKKL
Sequence of entity 4 (V), FASTA
>5XTC_4 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (chains V)
APKVFRQYWDIPDGTDCHRKAYSTTSIASVAGLTAAAYRVTLNPPGTFLEGVAKVGQYTF
TAAAVGAVFGLTTCISAHVREKPDDPLNYFLGGCAGGLTLGARTHNYGIGAAACVYFGIA
ASLVKMGRLEGWEVFAKPKV
Sequence of entity 5 (W), FASTA
>5XTC_5 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 (chains W)
GLSGYSMLAIGIGTLIYGHWSIMKWNRERRRLQIEDFEARIALLPLLQAETDRRTLQMLR
ENLEEEAIIMKDVPDWKVGESVFHTTRWVPPLIGELYGLRTTEEALHASHGFMWYT
Sequence of entity 6 (X), FASTA
>5XTC_6 Acyl carrier protein, mitochondrial (chains X)
PPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIP
DIDAEKLMCPQEIVDYIADKKDVYE
Sequence of entity 7 (Y), FASTA
>5XTC_7 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial (chains Y)
HIEPRYRQFPQLTRSQVFQSEFFSGLMWFWILWRFWHDSEEVLGHFPYPDPSQWTDEEL
Sequence of entity 8 (Z), FASTA
>5XTC_8 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 (chains Z)
GHHKMELPDYRQWKIEGTPLETIQKKLAAKGLRDPWGRNEAWRYMGGFAKSVSFSDVFFK
GFKWGFAAFVVAVGAEYYLE
Sequence of entity 9 (a), FASTA
>5XTC_9 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial (chains a)
KRLFVIRPSRFYDRRFLKLLRFYIALTGIPVAIFITLVNVFIGQAELAEIPEGYVPEHWE
YYKHPISRWIARNFYDSPEKIYERTMAVLQIEAEKAELRVKELEVRKLMHVRGDGPWYYY
ETIDKELIDHSPKATPDN
Sequence of entity 10 (b), FASTA
>5XTC_10 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 (chains b)
MTGYTPDEKLRLQQLRELRRRWLKDQELSPREPVLPPQKMGPMEKFWNKFLENKSPWRKM
VHGVYKKSIFVFTHVLVPVWIIHYYMKYHVSEKPYGIVEKKSRIFPGDTILETGEVIPPM
KEFPDQHH
Sequence of entity 11 (c), FASTA
>5XTC_11 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (chains c)
KDMFPGPYPRTPEERAAAAKKYNMRVEDYEPYPDDGMGYGDYPKLPDRSQHERDPWYSWD
QPGLRLNWGEPMHWHLDMYNRNRVDTSPTPVSWHVMCMQLFGFLAFMIFMCWVGDVYPVY
QPVGPKQYPYNNLYLERGGDPSKEPERVVHYEI
Sequence of entity 12 (d), FASTA
>5XTC_12 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 (chains d)
MPDSWDKDVYPEPPRRTPVQPNPIVYMMKAFDLIVDRPVTLVREFIERQHAKNRYYYYHR
QYRRVPDITECKEEDIMCMYEAEMQWKRDYKVDQEIINIMQDRLKACQQREGQNYQQNCI
KEVEQFTQVAKAYQDRYQDLGAYSSARKCLAKQRQRMLQERKAAKEAAAAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLX | (9R,11S)-9-({[(1S)-1-hydroxyhexadecyl]oxy}methyl)-2,2-dimethyl-5,7,10-trioxa-2L… | C42 H89 N O8 P | 9 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 5 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 4 |
| 8Q1 | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C23 H45 N2 O8 P S | 1 |
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 O75306 (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
- 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
About this viewer
MolViewer shows 5XTC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.