6RQF: Cytochrome b6
3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia oleracea with natively bound thylakoid lipids and plastoquinone molecules. Determined by electron microscopy at 3.58 Å resolution. Released 13 Nov 2019.
- Method
- Electron microscopy
- Resolution
- 3.58 Å
- Organism
- Spinacia oleracea
- Chains
- 16
- Atoms
- 16,359
- Mol. weight
- 232.71 kDa
- Ligands
- HEM, HEC, CLA, BCR
- Released
- 13 Nov 2019
Explore 6RQF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6RQF contains 81 α-helices and 100 β-strands across 16 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: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| α-helix | 15-22 | 8 | |
| β-strand | 25-26 | 2 | 17 |
| α-helix | 32-35 | 4 | |
| α-helix | 36-54 | 19 | |
| α-helix | 65-74 | 10 | |
| α-helix | 79-106 | 28 | |
| α-helix | 116-136 | 21 | |
| β-strand | 141 | 1 | 18 |
| α-helix | 142-152 | 11 | |
| α-helix | 154-157 | 4 | |
| α-helix | 160-162 | 3 | |
| α-helix | 163-170 | 8 | |
| α-helix | 177-185 | 9 | |
| α-helix | 186-190 | 5 | |
| α-helix | 191-209 | 19 | |
Chain B: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-19 | 8 | |
| β-strand | 29-30 | 2 | 17 |
| α-helix | 39-57 | 19 | |
| α-helix | 64 | 1 | |
| β-strand | 65 | 1 | 18 |
| α-helix | 66 | 1 | |
| α-helix | 79-81 | 3 | |
| α-helix | 82-88 | 7 | |
| α-helix | 94-108 | 15 | |
| α-helix | 111-114 | 4 | |
| α-helix | 127-146 | 20 | |
Chain C: 6 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-8 | 7 | |
| β-strand | 13 | 1 | 19 |
| β-strand | 19 | 1 | 19 |
| α-helix | 20-22 | 3 | |
| β-strand | 32-34 | 3 | 20 |
| β-strand | 38-39 | 2 | 21 |
| β-strand | 44-50 | 7 | 20 |
| β-strand | 59-60 | 2 | 22 |
| β-strand | 66-67 | 2 | 22 |
| β-strand | 70-76 | 7 | 21 |
| β-strand | 79 | 1 | 23 |
| β-strand | 81 | 1 | 23 |
| β-strand | 82-83 | 2 | 20 |
| α-helix | 84-85 | 2 | |
| α-helix | 91-97 | 7 | |
| β-strand | 103-104 | 2 | 21 |
| β-strand | 113-119 | 7 | 21 |
| β-strand | 125-131 | 7 | 20 |
| β-strand | 145-150 | 6 | 21 |
| β-strand | 153-154 | 2 | 21 |
| β-strand | 159 | 1 | 24 |
| β-strand | 165 | 1 | 24 |
| β-strand | 177-179 | 3 | 25 |
| β-strand | 182-184 | 3 | 26 |
| β-strand | 190-192 | 3 | 26 |
| β-strand | 195-196 | 2 | 25 |
| β-strand | 205-207 | 3 | 26 |
| α-helix | 212 | 1 | |
| β-strand | 213 | 1 | 27 |
| β-strand | 220-221 | 2 | 25 |
| β-strand | 228 | 1 | 27 |
| β-strand | 235-236 | 2 | 21 |
| β-strand | 239-245 | 7 | 21 |
| α-helix | 248-282 | 35 | |
Chain D: 7 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-25 | 14 | |
| α-helix | 27-39 | 13 | |
| β-strand | 53-54 | 2 | 28 |
| β-strand | 56 | 1 | 28 |
| β-strand | 62 | 1 | 28 |
| β-strand | 64 | 1 | 28 |
| α-helix | 65-71 | 7 | |
| α-helix | 73 | 1 | |
| β-strand | 77-81 | 5 | 28 |
| α-helix | 83-85 | 3 | |
| β-strand | 87-91 | 5 | 28 |
| β-strand | 92 | 1 | 29 |
| β-strand | 98 | 1 | 29 |
| β-strand | 101-104 | 4 | 28 |
| β-strand | 106 | 1 | 30 |
| α-helix | 112 | 1 | |
| β-strand | 113 | 1 | 30 |
| α-helix | 114-115 | 2 | |
| β-strand | 116 | 1 | 31 |
| β-strand | 123-125 | 3 | 31 |
| β-strand | 129-132 | 4 | 31 |
| β-strand | 138 | 1 | 31 |
| β-strand | 149-155 | 7 | 28 |
| β-strand | 158-163 | 6 | 28 |
| β-strand | 168 | 1 | 32 |
| β-strand | 173 | 1 | 32 |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-26 | 25 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-34 | 32 | |
Chains G and O: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-29 | 26 | |
Chains H and P: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-25 | 23 | |
6 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 |
|---|
| Cytochrome b6 | A, I | protein | 215 | Spinacia oleracea | P00165 (AlphaFold model) |
| Cytochrome b6-f complex subunit 4 | B, J | protein | 160 | Spinacia oleracea | P00166 (AlphaFold model) |
| Cytochrome f | C, K | protein | 285 | Spinacia oleracea | P16013 (AlphaFold model) |
| Cytochrome b6-f complex iron-sulfur subunit, chloroplastic | D, L | protein | 179 | Spinacia oleracea | P08980 (AlphaFold model) |
| Cytochrome b6-f complex subunit 6 | E, M | protein | 31 | Spinacia oleracea | Q9M3L0 |
| Cytochrome b6-f complex subunit 7 | F, N | protein | 36 | Spinacia oleracea | P80883 |
| Cytochrome b6-f complex subunit 5 | G, O | protein | 37 | Spinacia oleracea | P69461 |
| Cytochrome b6-f complex subunit 8 | H, P | protein | 29 | Spinacia oleracea | P61045 |
Sequence of entity 1 (A, I), FASTA
>6RQF_1 Cytochrome b6 (chains A, I)
MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRP
TVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVT
GVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTL
TRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL
Sequence of entity 2 (B, J), FASTA
>6RQF_2 Cytochrome b6-f complex subunit 4 (chains B, J)
MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPS
MIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKF
QNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF
Sequence of entity 3 (C, K), FASTA
>6RQF_3 Cytochrome f (chains C, K)
YPIFAQQGYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQV
LANGKKGGLNVGAVLILPEGFELAPPDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPG
QKYSEITFPILAPDPATKKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVK
KIVRKEKGGYEINIADASDGREVVDIIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGD
AEVVLQDPLRIQGLLFFFASVILAQIFLVLKKKQFEKVQLSEMNF
Sequence of entity 4 (D, L), FASTA
>6RQF_4 Cytochrome b6-f complex iron-sulfur subunit, chloroplastic (chains D, L)
ATSIPADNVPDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALG
NDVIAAEWLKTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAE
NKFICPCHGSQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA
Sequence of entity 5 (E, M), FASTA
>6RQF_5 Cytochrome b6-f complex subunit 6 (chains E, M)
MFTLTSYFGFLLAALTITSALFIGLNKIRLI
Sequence of entity 6 (F, N), FASTA
>6RQF_6 Cytochrome b6-f complex subunit 7 (chains F, N)
NAAAEIFRIAAVMNGLTLVGVAIGFVLLRIEATVEE
Sequence of entity 7 (G, O), FASTA
>6RQF_7 Cytochrome b6-f complex subunit 5 (chains G, O)
MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
Sequence of entity 8 (H, P), FASTA
>6RQF_8 Cytochrome b6-f complex subunit 8 (chains H, P)
MDIVSLAWAALMVVFTFSLSLVVWGRSGL
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 | 4 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 2 |
| BCR | Beta-carotene | C40 H56 | 2 |
| PL9 | 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-he… | C53 H80 O2 | 3 |
| 6PL | (4S,7R)-4-hydroxy-n,n,n-trimethyl-9-oxo-7-[(palmitoyloxy)methyl]-3,5,8-trioxa-4… | C42 H85 N O8 P | 3 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 2 |
| PGV | (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoylo… | C40 H77 O10 P | 4 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 3 |
Primary citation
Cryo-EM structure of the spinach cytochrome b6f complex at 3.6 angstrom resolution. Malone, L.A., Qian, P., Mayneord, G.E. et al. Nature (2019) 575:535-539. DOI 10.1038/s41586-019-1746-6 · PubMed
Other PDB entries of the same protein (UniProt P00165 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9ES7 1.94 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at…
- 7ZYV 2.13 Å, Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex…
- 9ES8 2.24 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f with decylplastoquinone bound at…
- 9ES9 2.33 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound…
- 7QRM 2.7 Å, Cryo-EM structure of catalytically active Spinacia oleracea cytochrome b6f in complex…
- 9TGG 3.18 Å, Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with bound plastocyanin
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