9ES9: Cytochrome b6
Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with inhibitor DBMIB bound at plastoquinol oxidation site. Determined by electron microscopy at 2.33 Å resolution. Released 16 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 2.33 Å
- Organism
- Spinacia oleracea
- Chains
- 18
- Atoms
- 16,450
- Mol. weight
- 285.36 kDa
- Ligands
- BCR, FES, SQD, CLA
- Released
- 16 Oct 2024
Explore 9ES9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9ES9 contains 86 α-helices and 94 β-strands across 18 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.
Chains A and I: 13 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-12 | 10 | |
| α-helix | 15-21 | 7 | |
| β-strand | 25-26 | 2 | 1 |
| α-helix | 32-35 | 4 | |
| α-helix | 36-54 | 19 | |
| α-helix | 65-74 | 10 | |
| α-helix | 79-106 | 28 | |
| α-helix | 115-136 | 22 | |
| β-strand | 141 | 1 | 2 |
| α-helix | 142-151 | 10 | |
| α-helix | 154-157 | 4 | |
| α-helix | 162-170 | 9 | |
| α-helix | 177-185 | 9 | |
| α-helix | 186-190 | 5 | |
| α-helix | 191-209 | 19 | |
Chains B and J: 9 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5 | 1 | 3 |
| α-helix | 12-19 | 8 | |
| β-strand | 28 | 1 | 3 |
| β-strand | 29-30 | 2 | 1 |
| α-helix | 40-57 | 18 | |
| α-helix | 59-61 | 3 | |
| β-strand | 65 | 1 | 2 |
| α-helix | 79-81 | 3 | |
| α-helix | 82-90 | 9 | |
| α-helix | 94-108 | 15 | |
| α-helix | 123-125 | 3 | |
| α-helix | 127-146 | 20 | |
| α-helix | 151-153 | 3 | |
Chains C and K: 7 helices, 25 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-8 | 7 | |
| β-strand | 13 | 1 | 4 |
| β-strand | 19 | 1 | 4 |
| α-helix | 20-23 | 4 | |
| β-strand | 28 | 1 | 5 |
| β-strand | 32-34 | 3 | 6 |
| β-strand | 38-39 | 2 | 5 |
| β-strand | 44-50 | 7 | 6 |
| β-strand | 59-60 | 2 | 7 |
| β-strand | 66-67 | 2 | 7 |
| β-strand | 70-76 | 7 | 5 |
| β-strand | 82-83 | 2 | 6 |
| α-helix | 84-85 | 2 | |
| α-helix | 86-88 | 3 | |
| α-helix | 91-96 | 6 | |
| β-strand | 103-106 | 4 | 5 |
| β-strand | 109-119 | 11 | 5 |
| β-strand | 125-131 | 7 | 6 |
| β-strand | 145-154 | 10 | 5 |
| β-strand | 159 | 1 | 8 |
| β-strand | 165 | 1 | 8 |
| β-strand | 172 | 1 | 9 |
| β-strand | 177-183 | 7 | 10 |
| β-strand | 190-194 | 5 | 10 |
| β-strand | 203-207 | 5 | 10 |
| α-helix | 212 | 1 | |
| β-strand | 213 | 1 | 11 |
| β-strand | 219-221 | 3 | 10 |
| β-strand | 226 | 1 | 9 |
| β-strand | 228 | 1 | 11 |
| β-strand | 235-245 | 11 | 5 |
| α-helix | 248-282 | 35 | |
Chains D and L: 9 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 12-39 | 28 | |
| α-helix | 43-45 | 3 | |
| β-strand | 54 | 1 | 12 |
| β-strand | 56 | 1 | 12 |
| β-strand | 62 | 1 | 12 |
| α-helix | 63 | 1 | |
| α-helix | 65-71 | 7 | |
| β-strand | 77-81 | 5 | 12 |
| α-helix | 83-85 | 3 | |
| β-strand | 87-91 | 5 | 12 |
| β-strand | 92 | 1 | 13 |
| β-strand | 98 | 1 | 13 |
| β-strand | 101-104 | 4 | 12 |
| β-strand | 106 | 1 | 14 |
| α-helix | 112 | 1 | |
| β-strand | 113 | 1 | 14 |
| α-helix | 114-115 | 2 | |
| β-strand | 116-117 | 2 | 15 |
| β-strand | 122-124 | 3 | 15 |
| β-strand | 131-132 | 2 | 15 |
| β-strand | 138-140 | 3 | 15 |
| α-helix | 146-148 | 3 | |
| β-strand | 149-153 | 5 | 12 |
| β-strand | 160-163 | 4 | 12 |
Chains E and M: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-27 | 26 | |
Chains F and N: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-36 | 35 | |
Chains G and O: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-31 | 28 | |
Chains H and P: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-25 | 23 | |
1 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 | 320 | Spinacia oleracea | P16013 (AlphaFold model) |
| Cytochrome b6-f complex iron-sulfur subunit, chloroplastic | D, L | protein | 230 | 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 | 131 | Spinacia oleracea | A0A9R0IV89 |
| 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 |
| Thylakoid soluble phosphoprotein | Q, R | protein | 103 | Spinacia oleracea | Q8GT36 |
Sequence of entity 1 (A, I), FASTA
>9ES9_1 Cytochrome b6 (chains A, I)
MSKVYDWFEERLEIQAIADDITSKYVPPHVNIFYCLGGITLTCFLVQVATGFAMTFYYRP
TVTDAFASVQYIMTEVNFGWLIRSVHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWVT
GVVLGVLTASFGVTGYSLPWDQIGYWAVKIVTGVPDAIPVIGSPLVELLRGSASVGQSTL
TRFYSLHTFVLPLLTAVFMLMHFLMIRKQGISGPL
Sequence of entity 2 (B, J), FASTA
>9ES9_2 Cytochrome b6-f complex subunit 4 (chains B, J)
MGVTKKPDLNDPVLRAKLAKGMGHNYYGEPAWPNDLLYIFPVVILGTIACNVGLAVLEPS
MIGEPADPFATPLEILPEWYFFPVFQILRTVPNKLLGVLLMASVPAGLLTVPFLENVNKF
QNPFRRPVATTVFLVGTVVALWLGIGATLPIDKSLTLGLF
Sequence of entity 3 (C, K), FASTA
>9ES9_3 Cytochrome f (chains C, K)
MQTINTFSWIKEQITRSISISLILYIITRSSIANAYPIFAQQGYENPREATGRIVCANCH
LANKPVDIEVPQAVLPDTVFEAVVRIPYDMQLKQVLANGKKGGLNVGAVLILPEGFELAP
PDRISPEMKEKMGNLSFQSYRPNKQNILVIGPVPGQKYSEITFPILAPDPATKKDVHFLK
YPIYVGGNRGRGQIYPDGSKSNNTVYNSTATGIVKKIVRKEKGGYEINIADASDGREVVD
IIPRGPELLVSEGESIKLDQPLTSNPNVGGFGQGDAEVVLQDPLRIQGLLFFFASVILAQ
IFLVLKKKQFEKVQLSEMNF
Sequence of entity 4 (D, L), FASTA
>9ES9_4 Cytochrome b6-f complex iron-sulfur subunit, chloroplastic (chains D, L)
MASFTLSSATPSQLCSSKNGMFAPSLALAKAGRVNVLISKERIRGMKLTCQATSIPADNV
PDMQKRETLNLLLLGALSLPTGYMLLPYASFFVPPGGGAGTGGTIAKDALGNDVIAAEWL
KTHAPGDRTLTQGLKGDPTYLVVESDKTLATFGINAVCTHLGCVVPFNAAENKFICPCHG
SQYNNQGRVVRGPAPLSLALAHCDVDDGKVVFVPWTETDFRTGEAPWWSA
Sequence of entity 5 (E, M), FASTA
>9ES9_5 Cytochrome b6-f complex subunit 6 (chains E, M)
MFTLTSYFGFLLAALTITSALFIGLNKIRLI
Sequence of entity 6 (F, N), FASTA
>9ES9_6 cytochrome b6-f complex subunit 7 (chains F, N)
MATAAASTTLSSAAVPAISGSRGQRKMNKVVYMSGVNSYGGLKANNAVLGLGQAVCTEQC
FANVVSSLRSTATKKGRSGGGGGAGGGALTSTCNAAAEIFRIAAVMNGLTLVGVAIGFVL
LRIEATVEEAE
Sequence of entity 7 (G, O), FASTA
>9ES9_7 Cytochrome b6-f complex subunit 5 (chains G, O)
MIEVFLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDL
Sequence of entity 8 (H, P), FASTA
>9ES9_8 Cytochrome b6-f complex subunit 8 (chains H, P)
MDIVSLAWAALMVVFTFSLSLVVWGRSGL
Sequence of entity 9 (Q, R), FASTA
>9ES9_9 Thylakoid soluble phosphoprotein (chains Q, R)
MSSLPFVFGAAASSRVVTAAAAKGTAETKQEKSFVDWLLGKITKEDQFYETDPILRGGDV
KSSGSTSGKKGGTTSGKKGTVSIPSKKKNGNGGVFGGLFAKKD
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCR | Beta-carotene | C40 H56 | 2 |
| 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 | 2 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 2 |
| BNT | 2,5-dibromo-3-isopropyl-6-methylbenzo-1,4-quinone | C10 H10 Br2 O2 | 2 |
| LMG | 1,2-distearoyl-monogalactosyl-diglyceride | C45 H86 O10 | 2 |
| UMQ | Undecyl-maltoside | C23 H44 O11 | 4 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 4 |
| HEM | Protoporphyrin IX containing FE | C34 H32 Fe N4 O4 | 4 |
Primary citation
Molecular basis of plastoquinone reduction in plant cytochrome b 6 f. Pintscher, S., Pietras, R., Mielecki, B. et al. Nat Plants (2024) 10:1814-1825. DOI 10.1038/s41477-024-01804-x · 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…
- 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
- 6RQF 3.58 Å, 3.6 Angstrom cryo-EM structure of the dimeric cytochrome b6f complex from Spinacia…
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