7VA9: Rba sphaeroides PufY-KO RC-LH1 dimer type-1
Rba sphaeroides PufY-KO RC-LH1 dimer type-1. Determined by electron microscopy at 3.08 Å resolution. Released 4 May 2022.
- Method
- Electron microscopy
- Resolution
- 3.08 Å
- Organism
- Cereibacter sphaeroides 2.4.1
- Chains
- 64
- Atoms
- 42,176
- Mol. weight
- 655.81 kDa
- Ligands
- BCL, BPB, U10, PC1
- Released
- 4 May 2022
Explore 7VA9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VA9 contains 205 α-helices and 62 β-strands across 64 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, 4, 8, aa, ab, b, B, e, E, g, G, j, J, n, N, p, P, r, R, t, T, v, V, x, X, z and Z: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-45 | 32 | |
Chains 1, 5, u, U, w, W, y and Y: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chains 3, 9, a, A, d, D, f, F, i, I, k, o, O and q: 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 6: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-45 | 3 | |
Chain 7: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-37 | 25 | |
Chains c and C: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 15-54 | 40 | |
| α-helix | 56-58 | 3 | |
| α-helix | 62-64 | 3 | |
Chains h and H: 10 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 22 |
| β-strand | 10 | 1 | 22 |
| α-helix | 12-34 | 23 | |
| β-strand | 43 | 1 | 14 |
| β-strand | 49 | 1 | 14 |
| α-helix | 50 | 1 | |
| α-helix | 57-61 | 5 | |
| β-strand | 62-66 | 5 | 23 |
| β-strand | 71-75 | 5 | 23 |
| β-strand | 87-89 | 3 | 24 |
| β-strand | 98-100 | 3 | 24 |
| α-helix | 104-107 | 4 | |
| α-helix | 110-112 | 3 | |
| β-strand | 123 | 1 | 25 |
| β-strand | 129 | 1 | 25 |
| β-strand | 131-133 | 3 | 26 |
| β-strand | 141-145 | 5 | 17 |
| β-strand | 152-154 | 3 | 26 |
| β-strand | 160-170 | 11 | 26 |
| β-strand | 175-182 | 8 | 26 |
| β-strand | 188-192 | 5 | 26 |
| α-helix | 193-195 | 3 | |
| β-strand | 197-198 | 2 | 26 |
| β-strand | 203-204 | 2 | 26 |
| α-helix | 210-213 | 4 | |
| α-helix | 217-219 | 3 | |
| α-helix | 227-243 | 17 | |
| α-helix | 251-259 | 9 | |
Chains K, Q, s and S: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-51 | 9 | |
2 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 | 1, 3, 5, 6, 7, 9, A, D, F, I, K, O, Q, S, U, W, Y, 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, 2, 4, 8, B, E, G, J, N, P, R, T, V, X, Z, 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
>7VA9_1 Reaction center protein L chain (chains L, l)
MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTW
NPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPF
AFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISF
FFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLS
AVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 2 (M, m), FASTA
>7VA9_2 Reaction center protein M chain (chains M, m)
MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLS
LFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIAS
FFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGI
FSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIA
DRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQ
NHGMAPLN
Sequence of entity 3 (H, h), FASTA
>7VA9_3 Reaction center protein H chain (chains H, h)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA
Sequence of entity 4 (1, 3, 5, 6, 7, 9, A, D, F, I, K, O, Q, S, U, W, Y, a, d, f, i, k, o, q, s, u, w, y), FASTA
>7VA9_4 Light-harvesting protein B-875 alpha chain (chains 1, 3, 5, 6, 7, 9, A, D, F, I, K, O, Q, S, U, W, Y, a, d, f, i, k, o, q, s, u, w, y)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 5 (0, 2, 4, 8, B, E, G, J, N, P, R, T, V, X, Z, aa, ab, b, e, g, j, n, p, r, t, v, x, z), FASTA
>7VA9_5 Light-harvesting protein B-875 beta chain (chains 0, 2, 4, 8, B, E, G, J, N, P, R, T, V, X, Z, aa, ab, b, e, g, j, n, p, r, t, v, x, z)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 6 (C, c), FASTA
>7VA9_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 | 64 |
| BPB | Bacteriopheophytin B | C55 H74 N4 O6 | 4 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 4 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 11 |
| FE2 | FE (II) ion | Fe | 2 |
| SPO | Spheroidene | C41 H60 O | 44 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 2 |
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…
Browse structure collections
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