Research workbench
Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A resolution
Analyse Cryo-EM structure of respiratory complex I from Yarrowia lipolytica at 3.2 A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RFR
- Type
- protein
- Length
- 8,057 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Yarrowia lipolytica
- Molecule
- Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I); Subunit NUBM of…
- EC
- 1.6.99.3, 7.1.1.2, 1.6.5.3
- UniProt
- Q9UUU3, Q9UUU2, Q9UUU1, A0A1D8NC63, A0A371BY45, A0A371C5F3, Q9UUU0, Q9UUT9, Q9UUT8, A0A371CB65, Q9UUT7, Q9B6D4, A0A1H6Q8Z5, A0A1H6PXT9, A0A1D8N3C8, A0A1D8NG21, A0A1D8NDL1, Q6ZY23, A0A371C2D0, A0A1H6PPE5, A0A1D8NKB4, A0A1D8N7X0, A0A1D8N3H5, A0A1D8ND94, A0A1D8NGI5, A0A371C0F2, A0A1D8N596, A0A1D8NFX6, A0A1H6PJS3, A0A1D8NJR0, A0A1D8N5V2, A0A1H6Q311, Q6ZY24, A0A371CFV9, S5U3V2, S5U4R9, S5TMS4, S5TMP9, S5TF58, Q9B6E9, A0A1H6PKH9, A0A1D8NNZ0
- Ligands
- 3PE, PLC, SF4, CDL, T7X, FES, LMN, ZMP, FMN, NDP, UQ9, CPL, ZN
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · resolution 3.2 · 42 distinct chains · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 692 | 27% helix, 15% strand | Q9UUU3 |
| B | Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3, 7.1.1.2) | protein | 456 | 44% helix, 15% strand | Q9UUU2 |
| C | Subunit NUCM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 438 | 40% helix, 11% strand | Q9UUU1 |
| D | Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 86 | 50% helix, 7% strand | A0A1D8NC63 |
| E | Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 349 | 34% helix, 14% strand | A0A371BY45 |
| F | Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 121 | 55% helix, 2% strand | A0A371C5F3 |
| G | Subunit NUGM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 239 | 20% helix, 23% strand | Q9UUU0 |
| H | Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 216 | 32% helix, 9% strand | Q9UUT9 |
| I | Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 190 | 30% helix, 13% strand | Q9UUT8 |
| J | Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 179 | 52% helix, 4% strand | A0A371CB65 |
| K | Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 177 | 33% helix, 10% strand | Q9UUT7 |
| L | Subunit NULM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 89 | 78% helix, 1% strand | Q9B6D4 |
| M | Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 117 | 15% helix, 20% strand | A0A1H6Q8Z5 |
| O | Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 77 | 52% helix, 3% strand | A0A1H6PXT9 |
| P | Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 123 | 54% helix, 0% strand | A0A1D8N3C8 |
| Q | Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 85 | 47% helix, 2% strand | A0A1D8NG21 |
| R | Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 106 | 51% helix, 1% strand | A0A1D8NDL1 |
| S | Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 174 | 63% helix, 0% strand | Q6ZY23 |
| U | Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 171 | 58% helix, 4% strand | A0A371C2D0 |
| W | Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 121 | 55% helix, 2% strand | A0A1H6PPE5 |
| X | Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 167 | 51% helix, 0% strand | A0A1D8NKB4 |
| Y | Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 123 | 16% helix, 20% strand | A0A1D8N7X0 |
| Z | Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 181 | 29% helix, 6% strand | A0A1D8N3H5 |
| a | Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 124 | 31% helix, 2% strand | A0A1D8ND94 |
| b | Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 64 | 80% helix, 0% strand | A0A1D8NGI5 |
| c | Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 44 | 43% helix, 0% strand | A0A371C0F2 |
| d | Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 90 | 61% helix, 2% strand | A0A1D8N596 |
| e | Subunit NUVM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 52 | 56% helix, 0% strand | A0A1D8NFX6 |
| f | Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 80 | 40% helix, 28% strand | A0A1H6PJS3 |
| g | Subunit NI9M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 76 | 49% helix, 0% strand | A0A1D8NJR0 |
| h | Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 136 | 21% helix, 8% strand | A0A1D8N5V2 |
| i | Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 83 | 47% helix, 4% strand | A0A1H6Q311 |
| j | Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.99.3) | protein | 90 | 42% helix, 6% strand | Q6ZY24 |
| n | Subunit NUNM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 114 | 56% helix, 0% strand | A0A371CFV9 |
| 1 | Subunit NU1M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 340 | 64% helix, 0% strand | S5U3V2 |
| 2 | Subunit NU2M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 1.6.5.3) | protein | 469 | 67% helix, 2% strand | S5U4R9 |
| 3 | Subunit NU3M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 127 | 51% helix, 2% strand | S5TMS4 |
| 4 | Subunit NU4M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 486 | 68% helix, 2% strand | S5TMP9 |
| 5 | Subunit NU5M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 654 | 74% helix, 3% strand | S5TF58 |
| 6 | Subunit NU6M of NADH:Ubiquinone Oxidoreductase (Complex I) (EC 7.1.1.2) | protein | 183 | 70% helix, 3% strand | Q9B6E9 |
| 8 | Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 82 | 72% helix, 0% strand | A0A1H6PKH9 |
| 9 | Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I) | protein | 86 | 49% helix, 6% strand | A0A1D8NNZ0 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 15 copies · chains C, I, W, g, 1, E, K, J, 4, 2, 5, S, b, 3, D, 6, i, a
- PLC · Diundecyl phosphatidyl choline · ligand · 7 copies · chains K, 1, I, W, U, g, Z, S, i, n, 4, 5, h, R
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, C, B, I, K
- CDL · Cardiolipin · ligand · 6 copies · chains E, 1, 3, X, g, 2, 6, D, I, Z, h, J, j, 5, S, i, n, 4
- T7X · Phosphatidylinositol · ligand · 4 copies · chains X, b, 2, L, 5, 6, E, K, 1, 3, C, J, j, 4
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, H
- LMN · Lauryl Maltose Neopentyl Glycol · ligand · 2 copies · chains J, 2, 4, a, j
- ZMP · S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate · ligand · 2 copies · chains O, P, Q, R
- FMN · Flavin mononucleotide · ligand · chains B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains E
- UQ9 · Ubiquinone-9 · ligand · chains C, K, 1
- CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · chains b, 2
- ZN · Zinc ion · metal · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.89 | 0.91 | 110 | UQ9 |
| 2 | 723 | 0.88 | 0.92 | 77 | NDP |
| 3 | 1191 | 0.88 | 0.89 | 113 | empty |
| 4 | 1163 | 0.87 | 0.88 | 119 | 3PE |
| 5 | 973 | 0.87 | 0.88 | 118 | 3PE |
Interfaces
201 interfaces between chains.
- B–H · 3541 Ų buried · 36 hydrogen bonds · protein-protein
- 1–3 · 3266 Ų buried · 14 hydrogen bonds · protein-protein
- L–6 · 3004 Ų buried · 17 hydrogen bonds · protein-protein
- G–Z · 2876 Ų buried · 27 hydrogen bonds · protein-protein
- C–G · 2791 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 6RFR · Cryo-EM structure of respiratory complex I from yarrowia lipolytica at 3.2 a resolution · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9UUU3
- Every structure of UniProt Q9UUU2
- Every structure of UniProt Q9UUU1
- Every structure of UniProt A0A1D8NC63
- Every structure of UniProt A0A371BY45
- Every structure of UniProt A0A371C5F3
- Every structure of UniProt Q9UUU0
- Every structure of UniProt Q9UUT9
- Every structure of UniProt Q9UUT8
- Every structure of UniProt A0A371CB65
- Every structure of UniProt Q9UUT7
- Every structure of UniProt Q9B6D4
- Every structure of UniProt A0A1H6Q8Z5
- Every structure of UniProt A0A1H6PXT9
- Every structure of UniProt A0A1D8N3C8
- Every structure of UniProt A0A1D8NG21
- Every structure of UniProt A0A1D8NDL1
- Every structure of UniProt Q6ZY23
- Every structure of UniProt A0A371C2D0
- Every structure of UniProt A0A1H6PPE5
- Every structure of UniProt A0A1D8NKB4
- Every structure of UniProt A0A1D8N7X0
- Every structure of UniProt A0A1D8N3H5
- Every structure of UniProt A0A1D8ND94
- Every structure of UniProt A0A1D8NGI5
- Every structure of UniProt A0A371C0F2
- Every structure of UniProt A0A1D8N596
- Every structure of UniProt A0A1D8NFX6
- Every structure of UniProt A0A1H6PJS3
- Every structure of UniProt A0A1D8NJR0
- Every structure of UniProt A0A1D8N5V2
- Every structure of UniProt A0A1H6Q311
- Every structure of UniProt Q6ZY24
- Every structure of UniProt A0A371CFV9
- Every structure of UniProt S5U3V2
- Every structure of UniProt S5U4R9
- Every structure of UniProt S5TMS4
- Every structure of UniProt S5TMP9
- Every structure of UniProt S5TF58
- Every structure of UniProt Q9B6E9
- Every structure of UniProt A0A1H6PKH9
- Every structure of UniProt A0A1D8NNZ0
- Elsewhere: RCSB PDB 6RFR · PDBe 6RFR · UniProt Q9UUU3 · UniProt Q9UUU2 · UniProt Q9UUU1 · UniProt A0A1D8NC63 · UniProt A0A371BY45 · UniProt A0A371C5F3 · UniProt Q9UUU0 · UniProt Q9UUT9 · UniProt Q9UUT8 · UniProt A0A371CB65 · UniProt Q9UUT7 · UniProt Q9B6D4 · UniProt A0A1H6Q8Z5 · UniProt A0A1H6PXT9 · UniProt A0A1D8N3C8 · UniProt A0A1D8NG21 · UniProt A0A1D8NDL1 · UniProt Q6ZY23 · UniProt A0A371C2D0 · UniProt A0A1H6PPE5 · UniProt A0A1D8NKB4 · UniProt A0A1D8N7X0 · UniProt A0A1D8N3H5 · UniProt A0A1D8ND94 · UniProt A0A1D8NGI5 · UniProt A0A371C0F2 · UniProt A0A1D8N596 · UniProt A0A1D8NFX6 · UniProt A0A1H6PJS3 · UniProt A0A1D8NJR0 · UniProt A0A1D8N5V2 · UniProt A0A1H6Q311 · UniProt Q6ZY24 · UniProt A0A371CFV9 · UniProt S5U3V2 · UniProt S5U4R9 · UniProt S5TMS4 · UniProt S5TMP9 · UniProt S5TF58 · UniProt Q9B6E9 · UniProt A0A1H6PKH9 · UniProt A0A1D8NNZ0
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