7VOY: Rba sphaeroides PufX-KO RC-LH1
Rba sphaeroides PufX-KO RC-LH1. Determined by electron microscopy at 4.2 Å resolution. Released 4 May 2022.
- Method
- Electron microscopy
- Resolution
- 4.2 Å
- Organism
- Cereibacter sphaeroides 2.4.1
- Chains
- 37
- Atoms
- 22,119
- Mol. weight
- 343.81 kDa
- Ligands
- BCL, BPH, U10, FE2
- Released
- 4 May 2022
Explore 7VOY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VOY contains 114 α-helices and 26 β-strands across 37 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 0, 2, 3, 5, 8, B, E, G, J, N, P, R, t, T, V, X and Z: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-45 | 32 | |
Chains 1 and S: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chains 4 and 6: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-51 | 9 | |
Chain 7: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-45 | 3 | |
Chain 9: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 6-10 | 5 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-51 | 9 | |
Chains A and D: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-10 | 5 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chain C: 5 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-10 | 4 | |
| α-helix | 13-37 | 25 | |
| α-helix | 39-41 | 3 | |
| α-helix | 43-50 | 8 | |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
8 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 |
|---|
| Light-harvesting protein B-875 alpha chain | 1, 4, 6, 7, 9, A, C, D, F, I, K, O, Q, S, U, W, Y | protein | 58 | Cereibacter sphaeroides 2.4.1 | Q3J1A4 (AlphaFold model) |
| Light-harvesting protein B-875 beta chain | 0, 2, 3, 5, 8, B, E, G, J, N, P, R, T, V, X, Z, t | protein | 49 | Cereibacter sphaeroides 2.4.1 | Q3J1A3 (AlphaFold model) |
| Reaction center protein L chain | L | protein | 282 | Cereibacter sphaeroides 2.4.1 | Q3J1A5 (AlphaFold model) |
| Reaction center protein M chain | M | protein | 308 | Cereibacter sphaeroides 2.4.1 | Q3J1A6 (AlphaFold model) |
| Reaction center protein H chain | H | protein | 260 | Cereibacter sphaeroides 2.4.1 | Q3J170 |
Sequence of entity 1 (1, 4, 6, 7, 9, A, C, D, F, I, K, O, Q, S, U, W, Y), FASTA
>7VOY_1 Light-harvesting protein B-875 alpha chain (chains 1, 4, 6, 7, 9, A, C, D, F, I, K, O, Q, S, U, W, Y)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 2 (0, 2, 3, 5, 8, B, E, G, J, N, P, R, T, V, X, Z, t), FASTA
>7VOY_2 Light-harvesting protein B-875 beta chain (chains 0, 2, 3, 5, 8, B, E, G, J, N, P, R, T, V, X, Z, t)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 3 (L), FASTA
>7VOY_3 Reaction center protein L chain (chains L)
MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTW
NPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPF
AFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISF
FFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLS
AVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 4 (M), FASTA
>7VOY_4 Reaction center protein M chain (chains M)
MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLS
LFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIAS
FFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGI
FSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIA
DRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQ
NHGMAPLN
Sequence of entity 5 (H), FASTA
>7VOY_5 Reaction center protein H chain (chains H)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 38 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 2 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 2 |
| FE2 | FE (II) ion | Fe | 1 |
| SPN | Speroidenone | C41 H70 O2 | 1 |
Primary citation
Structural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC-LH1 supercomplex. Cao, P., Bracun, L., Yamagata, A. et al. Nat Commun (2022) 13:1977-1977. DOI 10.1038/s41467-022-29563-3 · PubMed
Other PDB entries of the same protein (UniProt Q3J1A4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7PIL 2.5 Å, Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
- 7VY3 2.63 Å, Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides lacking…
- 7VOR 2.74 Å, The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-1
- 7VNY 2.79 Å, Rba sphaeroides WT RC-LH1 monomer
- 7VNM 2.86 Å, Rba sphaeroides PufY-KO RC-LH1 monomer
- 7VOT 2.9 Å, The structure of dimeric photosynthetic RC-LH1 supercomplex in Class-2
- 7F0L 2.94 Å, Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides monomer
- 7VA9 3.08 Å, Rba sphaeroides PufY-KO RC-LH1 dimer type-1
- 7VB9 3.45 Å, Rba sphaeroides PufY-KO RC-LH1 dimer type-2
Browse structure collections
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