1VF5: Cytochrome b6f Complex from M.laminosus
Crystal Structure of Cytochrome b6f Complex from M.laminosus. Determined by X-ray diffraction at 3.0 Å resolution. Released 20 Apr 2004.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Mastigocladus laminosus
- Chains
- 16
- Atoms
- 15,091
- Mol. weight
- 228.96 kDa
- Ligands
- HEM, HEC, TDS, PL9
- Released
- 20 Apr 2004
Explore 1VF5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1VF5 contains 70 α-helices and 63 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: 12 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 33-35 | 3 | |
| α-helix | 36-54 | 19 | |
| α-helix | 65-73 | 9 | |
| α-helix | 79-106 | 28 | |
| α-helix | 116-135 | 20 | |
| β-strand | 141 | 1 | 1 |
| α-helix | 142-152 | 11 | |
| α-helix | 154-156 | 3 | |
| α-helix | 161-170 | 10 | |
| α-helix | 178-185 | 8 | |
| α-helix | 186-190 | 5 | |
| α-helix | 191-204 | 14 | |
Chain B: 9 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-57 | 18 | |
| α-helix | 60 | 1 | |
| β-strand | 61 | 1 | 2 |
| α-helix | 62 | 1 | |
| α-helix | 64 | 1 | |
| β-strand | 65 | 1 | 1 |
| α-helix | 66 | 1 | |
| α-helix | 82-88 | 7 | |
| α-helix | 96-109 | 14 | |
| α-helix | 111-114 | 4 | |
| α-helix | 127-143 | 17 | |
Chain C: 7 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-8 | 7 | |
| β-strand | 14 | 1 | 3 |
| β-strand | 20 | 1 | 3 |
| α-helix | 21-24 | 4 | |
| β-strand | 29 | 1 | 4 |
| β-strand | 33-35 | 3 | 5 |
| β-strand | 39-40 | 2 | 2 |
| β-strand | 45-51 | 7 | 5 |
| β-strand | 60-61 | 2 | 6 |
| β-strand | 67-68 | 2 | 6 |
| β-strand | 72-73 | 2 | 7 |
| β-strand | 75-77 | 3 | 2 |
| β-strand | 83-84 | 2 | 5 |
| α-helix | 85-86 | 2 | |
| α-helix | 92-97 | 6 | |
| β-strand | 104-105 | 2 | 2 |
| β-strand | 113-115 | 3 | 2 |
| β-strand | 128-132 | 5 | 5 |
| β-strand | 145-153 | 9 | 2 |
| β-strand | 154-155 | 2 | 7 |
| β-strand | 160 | 1 | 8 |
| β-strand | 166 | 1 | 8 |
| β-strand | 182 | 1 | 9 |
| β-strand | 198 | 1 | 9 |
| β-strand | 220 | 1 | 10 |
| β-strand | 222 | 1 | 10 |
| β-strand | 240 | 1 | 4 |
| β-strand | 241-249 | 9 | 2 |
| α-helix | 252-275 | 24 | |
| α-helix | 277-279 | 3 | |
| α-helix | 283-285 | 3 | |
Chain D: 6 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-42 | 20 | |
| β-strand | 58 | 1 | 11 |
| α-helix | 66-71 | 6 | |
| β-strand | 80-81 | 2 | 11 |
| α-helix | 88 | 1 | |
| β-strand | 89-90 | 2 | 11 |
| β-strand | 93 | 1 | 12 |
| β-strand | 99 | 1 | 12 |
| β-strand | 105 | 1 | 11 |
| β-strand | 107 | 1 | 13 |
| α-helix | 113 | 1 | |
| β-strand | 114 | 1 | 13 |
| α-helix | 115-116 | 2 | |
| β-strand | 117 | 1 | 14 |
| β-strand | 124-125 | 2 | 14 |
| β-strand | 132-133 | 2 | 14 |
| α-helix | 147-148 | 2 | |
| β-strand | 149 | 1 | 11 |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-23 | 22 | |
Chains F and S: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-28 | 26 | |
Chains G and T: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-21 | 12 | |
| α-helix | 23-28 | 6 | |
Chains H and U: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-28 | 23 | |
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) |
| Subunit IV | B, O | protein | 160 | Mastigocladus laminosus | P83792 (AlphaFold model) |
| Cytochrome F | C, P | protein | 289 | Mastigocladus laminosus | P83793 (AlphaFold model) |
| Rieske iron-sulfur protein | D, Q | protein | 179 | Mastigocladus laminosus | P83794 (AlphaFold model) |
| Protein pet L | E, R | protein | 32 | Mastigocladus laminosus | P83795 |
| Protein pet M | F, S | protein | 35 | Mastigocladus laminosus | P83796 |
| Protein pet G | G, T | protein | 37 | Mastigocladus laminosus | P83797 |
| Protein pet N | H, U | protein | 29 | Mastigocladus laminosus | P83798 |
Sequence of entity 1 (A, N), FASTA
>1VF5_1 CYTOCHROME B6 (chains A, N)
MANVYDWFQERLEIQALADDVTSKYVPPHVNIFYCLGGITLTCFLIQFATGFAMTFYYKP
TVTEAYASVQYIMNEVSFGWLIRSIHRWSASMMVLMMILHVFRVYLTGGFKKPRELTWIS
GVILAVITVSFGVTGYSLPWDQVGYWAVKIVSGVPEAIPVVGVLISDLLRGGSSVGQATL
TRYYSAHTFVLPWLIAVFMLLHFLMIRKQGISGPL
Sequence of entity 2 (B, O), FASTA
>1VF5_2 SUBUNIT IV (chains B, O)
MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPA
MVGEPANPFATPLEILPEWYLYPVFQILRSLPNKLLGVLLMASVPLGLILVPFIENVNKF
QNPFRRPVATTIFLFGTLVTIWLGIGAALPLDKTLTLGLF
Sequence of entity 3 (C, P), FASTA
>1VF5_3 CYTOCHROME F (chains C, P)
YPFWAQQTYPPTPREPTGRIVCANCHLAAKPAEVEVPQSVLPDTVFKAVVKIPYDTKLQQ
VAADGSKVGLNVGAVLMLPEGFKIAPEERIPEELKKEVGDVYFQPYKEGQDNVLLVGPLP
GEQYQEIVFPVLSPNPTTDKNIHFGKYAIHLGANRGRGQIYPTGEKSNNNVFTASATGTI
TKIAKEEDEYGNVKYQVSIQTDSGKTVVDTIPAGPELIVSEGQAVKAGEALTNNPNVGGF
GQDDTEIVLQDPNRVKWMIAFICLVMLAQLMLILKKKQVEKVQAAEMNF
Sequence of entity 4 (D, Q), FASTA
>1VF5_4 RIESKE IRON-SULFUR PROTEIN (chains D, Q)
MAQFTESMDVPDMGRRQFMNLLAFGTVTGVALGALYPLVKYFIPPSGGAVGGGTTAKDKL
GNNVKVSKFLESHNAGDRVLVQGLKGDPTYIVVESKEAIRDYGINAVCTHLGCVVPWNAA
ENKFKCPCHGSQYDETGRVIRGPAPLSLALCHATVQDDNIVLTPWTETDFRTGEKPWWV
Sequence of entity 5 (E, R), FASTA
>1VF5_5 PROTEIN PET L (chains E, R)
MILGAVFYIVFIALFFGIAVGIIFAIKSIKLI
Sequence of entity 6 (F, S), FASTA
>1VF5_6 PROTEIN PET M (chains F, S)
MTEEMLYAALLSFGLIFVGWGLGVLLLKIQGAEKE
Sequence of entity 7 (G, T), FASTA
>1VF5_7 PROTEIN PET G (chains G, T)
MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG
Sequence of entity 8 (H, U), FASTA
>1VF5_8 PROTEIN PET N (chains H, U)
MEIDVLGWVALLVVFTWSIAMVVWGRNGL
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 |
| TDS | 8-hydroxy-5,7-dimethoxy-3-methyl-2-tridecyl-4H-chromen-4-one | C25 H38 O5 | 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 | 2 |
| 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 |
| CLA | Chlorophyll a | C55 H72 Mg N4 O5 | 2 |
| FES | FE2/S2 (inorganic) cluster | Fe2 S2 | 2 |
| BCR | Beta-carotene | C40 H56 | 2 |
Primary citation
Structure of the Cytochrome B6F Complex of Oxygenic Photosynthesis: Tuning the Cavity. Kurisu, G., Zhang, H., Smith, J.L. et al. Science (2003) 302:1009-1014. DOI 10.1126/science.1090165 · 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…
- 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…
- 2D2C 3.8 Å, Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus
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