7VNY: Rba sphaeroides WT RC-LH1 monomer
Rba sphaeroides WT RC-LH1 monomer. Determined by electron microscopy at 2.79 Å resolution. Released 1 Jun 2022.
- Method
- Electron microscopy
- Resolution
- 2.79 Å
- Organism
- Cereibacter sphaeroides 2.4.1
- Chains
- 33
- Atoms
- 22,472
- Mol. weight
- 341.69 kDa
- Ligands
- BPB, BCL, CDL, SPO
- Released
- 1 Jun 2022
Explore 7VNY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VNY contains 108 α-helices and 32 β-strands across 33 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, 8, B, C, E, G, J, N, P, R, T, V and Z: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-45 | 32 | |
Chain 1: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-51 | 9 | |
Chain 3: 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 7: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-36 | 24 | |
Chains 9, A, I, O and S: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chains D and K: 4 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 | 43-50 | 8 | |
Chain F: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chain H: 10 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7 | 1 | 9 |
| β-strand | 10 | 1 | 9 |
| α-helix | 12-35 | 24 | |
| β-strand | 43 | 1 | 1 |
| β-strand | 49 | 1 | 1 |
| α-helix | 50 | 1 | |
| α-helix | 57-61 | 5 | |
| β-strand | 62-66 | 5 | 10 |
| α-helix | 67-69 | 3 | |
| β-strand | 71-75 | 5 | 10 |
| β-strand | 87-89 | 3 | 11 |
| β-strand | 98-100 | 3 | 11 |
| α-helix | 104-107 | 4 | |
| α-helix | 110-112 | 3 | |
| β-strand | 123 | 1 | 12 |
| β-strand | 129 | 1 | 12 |
| β-strand | 131-133 | 3 | 13 |
| β-strand | 141-142 | 2 | 4 |
| β-strand | 152-154 | 3 | 13 |
| β-strand | 160-170 | 11 | 13 |
| β-strand | 175-182 | 8 | 13 |
| β-strand | 188-192 | 5 | 13 |
| α-helix | 193-195 | 3 | |
| β-strand | 197-198 | 2 | 13 |
| β-strand | 203-204 | 2 | 13 |
| α-helix | 211-215 | 5 | |
| α-helix | 217-218 | 2 | |
| α-helix | 227-243 | 17 | |
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 |
|---|
| 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 (AlphaFold model) |
| Light-harvesting protein B-875 alpha chain | 1, 3, 7, 9, A, D, F, I, K, O, Q, S, U, W | protein | 58 | Cereibacter sphaeroides 2.4.1 | Q3J1A4 (AlphaFold model) |
| Light-harvesting protein B-875 beta chain | 0, 2, 8, B, C, E, G, J, N, P, R, T, V, Z | protein | 49 | Cereibacter sphaeroides 2.4.1 | Q3J1A3 |
| Intrinsic membrane protein PufX | X | protein | 82 | Cereibacter sphaeroides 2.4.1 | P13402 |
| Rsp_7571 Protein-Y PufY | Y | protein | 53 | Cereibacter sphaeroides 2.4.1 | U5NME9 |
Sequence of entity 1 (L), FASTA
>7VNY_1 Reaction center protein L chain (chains L)
MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTW
NPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPF
AFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISF
FFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLS
AVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 2 (M), FASTA
>7VNY_2 Reaction center protein M chain (chains M)
MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLS
LFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIAS
FFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGI
FSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIA
DRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQ
NHGMAPLN
Sequence of entity 3 (H), FASTA
>7VNY_3 Reaction center protein H chain (chains H)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA
Sequence of entity 4 (1, 3, 7, 9, A, D, F, I, K, O, Q, S, U, W), FASTA
>7VNY_4 Light-harvesting protein B-875 alpha chain (chains 1, 3, 7, 9, A, D, F, I, K, O, Q, S, U, W)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 5 (0, 2, 8, B, C, E, G, J, N, P, R, T, V, Z), FASTA
>7VNY_5 Light-harvesting protein B-875 beta chain (chains 0, 2, 8, B, C, E, G, J, N, P, R, T, V, Z)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 6 (X), FASTA
>7VNY_6 Intrinsic membrane protein PufX (chains X)
MADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQEN
QAPAPNITGALETGIELIKHLV
Sequence of entity 7 (Y), FASTA
>7VNY_7 Rsp_7571 Protein-Y PufY (chains Y)
MPEVSEFAFRLMMAAVIFVGVGIMFAFAGGHWFVGLVVGGLVAAFFAATPNSN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BPB | Bacteriopheophytin B | C55 H74 N4 O6 | 2 |
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 32 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 2 |
| SPO | Spheroidene | C41 H60 O | 26 |
| FE2 | FE (II) ion | Fe | 1 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 4 |
| PC1 | 1,2-diacyl-sn-glycero-3-phosphocholine | C44 H88 N O8 P | 9 |
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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