4PV1: Cytochrome b6
Cytochrome B6F structure from M. laminosus with the quinone analog inhibitor stigmatellin. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Aug 2014.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Mastigocladus laminosus
- Chains
- 8
- Atoms
- 8,049
- Mol. weight
- 118.2 kDa
- Ligands
- MYS, CD, HEC, UMQ
- Released
- 20 Aug 2014
Explore 4PV1 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4PV1 contains 41 α-helices and 39 β-strands across 8 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: 13 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-12 | 8 | |
| 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 | 79-105 | 27 | |
| α-helix | 115-136 | 22 | |
| β-strand | 141 | 1 | 2 |
| α-helix | 142-151 | 10 | |
| α-helix | 154-156 | 3 | |
| α-helix | 162-170 | 9 | |
| α-helix | 177-185 | 9 | |
| α-helix | 186-190 | 5 | |
| α-helix | 191-209 | 19 | |
Chain B: 11 helices, 5 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 | |
| β-strand | 61 | 1 | 4 |
| α-helix | 64 | 1 | |
| β-strand | 65 | 1 | 2 |
| α-helix | 66 | 1 | |
| α-helix | 71-72 | 2 | |
| α-helix | 79-81 | 3 | |
| α-helix | 82-90 | 9 | |
| α-helix | 94-110 | 17 | |
| α-helix | 115-117 | 3 | |
| α-helix | 127-146 | 20 | |
| α-helix | 151-153 | 3 | |
Chain C: 7 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-8 | 7 | |
| α-helix | 21-24 | 4 | |
| β-strand | 33-35 | 3 | 5 |
| β-strand | 39-40 | 2 | 4 |
| β-strand | 45-51 | 7 | 5 |
| β-strand | 60-61 | 2 | 6 |
| β-strand | 67-68 | 2 | 6 |
| β-strand | 71-77 | 7 | 4 |
| α-helix | 78-79 | 2 | |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 85-86 | 2 | |
| α-helix | 87-89 | 3 | |
| α-helix | 92-98 | 7 | |
| β-strand | 104-105 | 2 | 4 |
| β-strand | 113-120 | 8 | 4 |
| β-strand | 126-132 | 7 | 5 |
| β-strand | 145-155 | 11 | 4 |
| β-strand | 160 | 1 | 7 |
| β-strand | 166 | 1 | 7 |
| β-strand | 194-195 | 2 | 8 |
| β-strand | 198 | 1 | 9 |
| β-strand | 208 | 1 | 9 |
| β-strand | 211-212 | 2 | 8 |
| β-strand | 239-249 | 11 | 4 |
| α-helix | 252-283 | 32 | |
Chain D: 6 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-42 | 30 | |
| β-strand | 57 | 1 | 10 |
| α-helix | 66-69 | 4 | |
| β-strand | 79-82 | 4 | 10 |
| α-helix | 84-86 | 3 | |
| β-strand | 88-91 | 4 | 10 |
| β-strand | 102 | 1 | 11 |
| β-strand | 104-105 | 2 | 10 |
| β-strand | 107 | 1 | 12 |
| α-helix | 113 | 1 | |
| β-strand | 114 | 1 | 12 |
| α-helix | 115-116 | 2 | |
| β-strand | 117-118 | 2 | 13 |
| β-strand | 123-124 | 2 | 13 |
| β-strand | 125 | 1 | 14 |
| β-strand | 132 | 1 | 14 |
| β-strand | 141 | 1 | 14 |
| α-helix | 147-149 | 3 | |
| β-strand | 151-153 | 3 | 11 |
| β-strand | 162-164 | 3 | 11 |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-27 | 25 | |
Chain F: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-30 | 28 | |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-30 | 27 | |
Chain H: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-25 | 23 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cytochrome b6 | A | protein | 215 | Mastigocladus laminosus | P83791 (AlphaFold model) |
| Cytochrome b6-f complex subunit 4 | B | protein | 160 | Mastigocladus laminosus | P83792 (AlphaFold model) |
| Apocytochrome f | C | protein | 289 | Mastigocladus laminosus | P83793 (AlphaFold model) |
| Cytochrome b6-f complex iron-sulfur subunit | D | protein | 179 | Mastigocladus laminosus | P83794 (AlphaFold model) |
| Cytochrome b6-f complex subunit 6 | E | protein | 32 | Mastigocladus laminosus | P83795 |
| Cytochrome b6-f complex subunit 7 | F | protein | 35 | Mastigocladus laminosus | P83796 |
| Cytochrome b6-f complex subunit 5 | G | protein | 37 | Mastigocladus laminosus | P83797 |
| Cytochrome b6-f complex subunit 8 | H | protein | 29 | Mastigocladus laminosus | P83798 |
Sequence of entity 1 (A), FASTA
>4PV1_1 Cytochrome b6 (chains A)
MANVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKP
TVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWIS
GVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATL
TRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL
Sequence of entity 2 (B), FASTA
>4PV1_2 Cytochrome b6-f complex subunit 4 (chains B)
MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPA
MVGEPADPFATPLEILPEWYLYPVFQILRSVPNKLLGVLLMASVPLGLILVPFIENVNKF
QNPFRRPVATTIFLFGTLVTIWLGIGATFPLDKTLTLGLF
Sequence of entity 3 (C), FASTA
>4PV1_3 Apocytochrome f (chains C)
YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQ
VAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLP
GEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTI
TKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGF
GQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMNF
Sequence of entity 4 (D), FASTA
>4PV1_4 Cytochrome b6-f complex iron-sulfur subunit (chains D)
MAQFTESMDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKL
GNNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAA
ENKFKCPCHGSQYDETGKVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGEKPWWV
Sequence of entity 5 (E), FASTA
>4PV1_5 Cytochrome b6-f complex subunit 6 (chains E)
MILGAVFYIVFIALFFGIAVGIIFAIKSIKLI
Sequence of entity 6 (F), FASTA
>4PV1_6 Cytochrome b6-f complex subunit 7 (chains F)
MTEEMLYAALLSFGLIFVGWGLGVLLLKIQGAEKE
Sequence of entity 7 (G), FASTA
>4PV1_7 Cytochrome b6-f complex subunit 5 (chains G)
MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG
Sequence of entity 8 (H), FASTA
>4PV1_8 Cytochrome b6-f complex subunit 8 (chains H)
MEIDVLGWVALLVVFTWSIAMVVWGRNGL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MYS | Pentadecane | C15 H32 | 1 |
| CD | Cadmium ion | Cd | 2 |
| HEC | Heme C | C34 H36 Fe N4 O4 | 4 |
| UMQ | Undecyl-maltoside | C23 H44 O11 | 3 |
| SMA | Stigmatellin a | C30 H42 O7 | 1 |
| 7PH | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate | C29 H57 O8 P | 1 |
| 8K6 | Octadecane | C18 H38 | 1 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 1 |
| 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 | 3 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 1 |
| BCR | Beta-carotene | C40 H56 | 1 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 1 |
Primary citation
Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Hasan, S.S., Proctor, E.A., Yamashita, E. et al. Biophys J (2014) 107:1620-1628. DOI 10.1016/j.bpj.2014.08.003 · 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
- 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…
- 2D2C 3.8 Å, Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus
Browse structure collections
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