7VB9: Rba sphaeroides PufY-KO RC-LH1 dimer type-2
Rba sphaeroides PufY-KO RC-LH1 dimer type-2. Determined by electron microscopy at 3.45 Å resolution. Released 4 May 2022.
- Method
- Electron microscopy
- Resolution
- 3.45 Å
- Organism
- Cereibacter sphaeroides 2.4.1
- Chains
- 51
- Atoms
- 36,474
- Mol. weight
- 556.33 kDa
- Ligands
- BCL, BPH, U10, FE2
- Released
- 4 May 2022
Explore 7VB9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VB9 contains 182 α-helices and 70 β-strands across 51 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, 4, 8, aa, ab, b, B, e, E, g, G, j, J, n, N, p, r, t, v, x and z: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-45 | 32 | |
Chains 5 and y: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-37 | 24 | |
| α-helix | 43-50 | 8 | |
Chains 6 and 7: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
| α-helix | 13-37 | 25 | |
Chain 9: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-51 | 9 | |
Chains a and A: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chain c: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-5 | 3 | |
| α-helix | 10-12 | 3 | |
| α-helix | 15-54 | 40 | |
| α-helix | 62-64 | 3 | |
Chain C: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 15-54 | 40 | |
Chains d, D, f, F, i, I, k, o, q, Q, s and u: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
6 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 |
|---|
| Reaction center protein L chain | L, l | protein | 282 | Cereibacter sphaeroides 2.4.1 | Q3J1A5 (AlphaFold model) |
| Reaction center protein M chain | M, m | protein | 308 | Cereibacter sphaeroides 2.4.1 | Q3J1A6 (AlphaFold model) |
| Reaction center protein H chain | H, h | protein | 260 | Cereibacter sphaeroides 2.4.1 | Q3J170 (AlphaFold model) |
| Light-harvesting protein B-875 alpha chain | 5, 6, 7, 9, A, D, F, I, K, O, Q, a, 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, 4, 8, B, E, G, J, N, aa, ab, b, e, g, j, n, p, r, t, v, x, z | protein | 49 | Cereibacter sphaeroides 2.4.1 | Q3J1A3 |
| Intrinsic membrane protein PufX | C, c | protein | 82 | Cereibacter sphaeroides 2.4.1 | P13402 |
Sequence of entity 1 (L, l), FASTA
>7VB9_1 Reaction center protein L chain (chains L, l)
MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTW
NPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPF
AFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISF
FFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLS
AVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 2 (M, m), FASTA
>7VB9_2 Reaction center protein M chain (chains M, m)
MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLS
LFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIAS
FFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGI
FSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIA
DRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQ
NHGMAPLN
Sequence of entity 3 (H, h), FASTA
>7VB9_3 Reaction center protein H chain (chains H, h)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA
Sequence of entity 4 (5, 6, 7, 9, A, D, F, I, K, O, Q, a, d, f, i, k, o, q, s, u, w, y), FASTA
>7VB9_4 Light-harvesting protein B-875 alpha chain (chains 5, 6, 7, 9, A, D, F, I, K, O, Q, a, d, f, i, k, o, q, s, u, w, y)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 5 (0, 4, 8, B, E, G, J, N, aa, ab, b, e, g, j, n, p, r, t, v, x, z), FASTA
>7VB9_5 Light-harvesting protein B-875 beta chain (chains 0, 4, 8, B, E, G, J, N, aa, ab, b, e, g, j, n, p, r, t, v, x, z)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 6 (C, c), FASTA
>7VB9_6 Intrinsic membrane protein PufX (chains C, c)
MADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQEN
QAPAPNITGALETGIELIKHLV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 51 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 4 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 4 |
| FE2 | FE (II) ion | Fe | 2 |
| SPO | Spheroidene | C41 H60 O | 36 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 9 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 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 Q3J1A5 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7P2C 2.04 Å, F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides…
- 7OD5 2.1 Å, F(M197)H mutant structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides…
- 4IN5 2.2 Å, (M)L214G mutant of the Rhodobacter sphaeroides Reaction Center
- 7MH3 2.3 Å, Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant;…
- 5LRI 2.4 Å, Photosynthetic reaction center mutant with GLUL212 replaced with trp (chain L, EL212W)
- 8C87 2.45 Å, Double mutant A(L172)C/L(L246)C structure of Photosynthetic Reaction Center From…
- 7MH4 2.48 Å, Crystal structure of R. sphaeroides Photosynthetic Reaction Center variant;…
- 7PIL 2.5 Å, Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A
- 8C3F 2.6 Å, Double mutant I(L177)H/F(M197)H structure of Photosynthetic Reaction Center From…
- 8C5X 2.6 Å, Double mutant A(L37)C/S(L99)C structure of Photosynthetic Reaction Center From…
- 8C7C 2.6 Å, Double mutant V(M84)C/A(L278)C structure of Photosynthetic Reaction Center From…
- 2WX5 2.63 Å, Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides…
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