2D2C: Cytochrome b6
Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus. Determined by X-ray diffraction at 3.8 Å resolution. Released 13 Dec 2005.
- Method
- X-ray diffraction
- Resolution
- 3.8 Å
- Organism
- Mastigocladus laminosus
- Chains
- 16
- Atoms
- 14,984
- Mol. weight
- 227.28 kDa
- Ligands
- HEC, OPC, FES, BCR
- Released
- 13 Dec 2005
Explore 2D2C in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
2D2C contains 74 α-helices and 52 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: 11 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-53 | 18 | |
| α-helix | 66-74 | 9 | |
| α-helix | 79-105 | 27 | |
| α-helix | 119-135 | 17 | |
| α-helix | 143-146 | 4 | |
| α-helix | 154-156 | 3 | |
| α-helix | 160-162 | 3 | |
| α-helix | 163-170 | 8 | |
| α-helix | 179-184 | 6 | |
| α-helix | 185-189 | 5 | |
| α-helix | 191-205 | 15 | |
Chain B: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-57 | 18 | |
| α-helix | 83-90 | 8 | |
| α-helix | 94-102 | 9 | |
| α-helix | 106-109 | 4 | |
| α-helix | 111-114 | 4 | |
| α-helix | 127-133 | 7 | |
| α-helix | 138-141 | 4 | |
Chain C: 6 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-7 | 5 | |
| β-strand | 14 | 1 | 1 |
| β-strand | 20 | 1 | 1 |
| α-helix | 21-24 | 4 | |
| β-strand | 39-40 | 2 | 2 |
| β-strand | 44-46 | 3 | 3 |
| β-strand | 60 | 1 | 4 |
| β-strand | 68 | 1 | 4 |
| β-strand | 75-77 | 3 | 2 |
| β-strand | 83-84 | 2 | 3 |
| α-helix | 92-96 | 5 | |
| β-strand | 113-115 | 3 | 2 |
| β-strand | 131-133 | 3 | 3 |
| β-strand | 146-151 | 6 | 2 |
| β-strand | 160 | 1 | 5 |
| β-strand | 166 | 1 | 5 |
| β-strand | 184-185 | 2 | 6 |
| β-strand | 195-196 | 2 | 6 |
| β-strand | 243-249 | 7 | 2 |
| α-helix | 252-274 | 23 | |
| α-helix | 276-279 | 4 | |
| α-helix | 283-285 | 3 | |
Chains D and Q: 5 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-21 | 3 | |
| α-helix | 23-33 | 11 | |
| α-helix | 36-41 | 6 | |
| β-strand | 65 | 1 | 7 |
| α-helix | 66-68 | 3 | |
| β-strand | 78-80 | 3 | 8 |
| β-strand | 89 | 1 | 9 |
| β-strand | 90-92 | 3 | 8 |
| β-strand | 93 | 1 | 10 |
| β-strand | 99 | 1 | 10 |
| β-strand | 105 | 1 | 9 |
| α-helix | 115-117 | 3 | |
| β-strand | 132 | 1 | 11 |
| β-strand | 141 | 1 | 11 |
| β-strand | 159 | 1 | 7 |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-4 | 3 | |
| α-helix | 5-8 | 4 | |
| α-helix | 12-15 | 4 | |
| α-helix | 23-26 | 4 | |
Chains F and S: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-26 | 23 | |
Chains G and T: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-14 | 4 | |
| α-helix | 18-22 | 5 | |
Chain H: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-7 | 4 | |
| α-helix | 10-25 | 16 | |
5 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, N | protein | 215 | Mastigocladus laminosus | P83791 (AlphaFold model) |
| Cytochrome b6-f complex subunit 4 | B, O | protein | 160 | Mastigocladus laminosus | P83792 (AlphaFold model) |
| Apocytochrome f | C, P | protein | 289 | Mastigocladus laminosus | P83793 (AlphaFold model) |
| Cytochrome b6-f complex iron-sulfur subunit | D, Q | protein | 179 | Mastigocladus laminosus | P83794 (AlphaFold model) |
| Cytochrome b6-f complex subunit VI | E, R | protein | 32 | Mastigocladus laminosus | P83795 |
| Cytochrome b6-f complex subunit VII | F, S | protein | 35 | Mastigocladus laminosus | P83796 |
| Cytochrome b6-f complex subunit V | G, T | protein | 37 | Mastigocladus laminosus | P83797 |
| Cytochrome b6-f complex subunit VIII | H, U | protein | 29 | Mastigocladus laminosus | P83798 |
Sequence of entity 1 (A, N), FASTA
>2D2C_1 Cytochrome b6 (chains A, N)
MANVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKP
TVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWIS
GVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATL
TRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL
Sequence of entity 2 (B, O), FASTA
>2D2C_2 Cytochrome b6-f complex subunit 4 (chains B, O)
MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPA
MVGEPANPFATPLEILPEWYLYPVFQILRSLPNKLLGVLLMASVPLGLILVPFIENVNKF
QNPFRRPVATTIFLFGTLVTIWLGIGAALPLDKTLTLGLF
Sequence of entity 3 (C, P), FASTA
>2D2C_3 Apocytochrome f (chains C, P)
YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQ
VAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLP
GEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTI
TKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGF
GQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMNF
Sequence of entity 4 (D, Q), FASTA
>2D2C_4 Cytochrome b6-f complex iron-sulfur subunit (chains D, Q)
MAQFTESMDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKL
GNNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAA
ENKFKCPCHGSQYDETGRVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGEKPWWV
Sequence of entity 5 (E, R), FASTA
>2D2C_5 Cytochrome b6-f complex subunit VI (chains E, R)
MILGAVFYIVFIALFFGIAVGIIFAIKSIKLI
Sequence of entity 6 (F, S), FASTA
>2D2C_6 Cytochrome b6-f complex subunit VII (chains F, S)
MTEEMLYAALLSFGLIFVGWGLGVLLLKIQGAEKE
Sequence of entity 7 (G, T), FASTA
>2D2C_7 Cytochrome b6-f complex subunit V (chains G, T)
MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG
Sequence of entity 8 (H, U), FASTA
>2D2C_8 Cytochrome b6-f complex subunit VIII (chains H, U)
MEIDVLGWVALLVVFTWSIAMVVWGRNGL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| HEC | Heme C | C34 H36 Fe N4 O4 | 8 |
| OPC | (7R,17E)-4-hydroxy-N,N,N,7-tetramethyl-7-[(8E)-octadec-8-enoyloxy]-10-oxo-3,5,9… | C45 H87 N O8 P | 4 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| BCR | Beta-carotene | C40 H56 | 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 |
Primary citation
Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex. Yan, J., Kurisu, G., Cramer, W.A. Proc Natl Acad Sci U S A (2006) 103:69-74. DOI 10.1073/pnas.0504909102 · PubMed
Other PDB entries of the same protein (UniProt P83791 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 4I7Z 2.8 Å, Crystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein…
- 1VF5 3.0 Å, Crystal Structure of Cytochrome b6f Complex from M.laminosus
- 2E74 3.0 Å, Crystal Structure of the Cytochrome b6f Complex from M.laminosus
- 4PV1 3.0 Å, Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin
- 4H13 3.07 Å, Crystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS
- 4H0L 3.25 Å, Cytochrome b6f Complex Crystal Structure from Mastigocladus laminosus with n-Side…
- 2E76 3.41 Å, Crystal Structure of the Cytochrome b6f Complex with tridecyl-stigmatellin (TDS) from…
- 2E75 3.55 Å, Crystal Structure of the Cytochrome b6f Complex with 2-nonyl-4-hydroxyquinoline N-oxide…
Browse structure collections
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