4V9G: Light-harvesting protein B-875 alpha chain
RC-LH1-PufX dimer complex from Rhodobacter sphaeroides. Determined by X-ray diffraction at 7.78 Å resolution. Released 9 Jul 2014.
- Method
- X-ray diffraction
- Resolution
- 7.78 Å
- Organism
- Rhodobacter sphaeroides
- Chains
- 64
- Atoms
- 38,108
- Mol. weight
- 619.06 kDa
- Ligands
- BCL, BPH, U10, PO4
- Released
- 9 Jul 2014
Explore 4V9G in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4V9G contains 173 α-helices and 31 β-strands across 61 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 A1: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-35 | 4 | |
Chain A2: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-17 | 5 | |
| α-helix | 21-24 | 4 | |
| α-helix | 29-36 | 8 | |
| α-helix | 43-45 | 3 | |
Chain A3: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-19 | 4 | |
| α-helix | 23-29 | 7 | |
Chain A4: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-36 | 6 | |
| α-helix | 40-42 | 3 | |
Chain A5: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-15 | 4 | |
Chain A6: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 38-40 | 3 | |
Chain A8: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 33-37 | 5 | |
| α-helix | 38-40 | 3 | |
Chain A9: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 33-38 | 6 | |
53 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 | A1, A2, A3, A5, A7, AD, AF, AJ, AN, AP, AT, AV, AX, AZ, B1, B2, B3, B5, B7, BD, BF, BJ, BN, BP, BT, BV, BX, BZ | protein | 58 | Rhodobacter sphaeroides | P0C0X9 (AlphaFold model) |
| Intrinsic membrane protein PufX | AB, BB | protein | 82 | Rhodobacter sphaeroides | P13402 (AlphaFold model) |
| Light-harvesting protein B-875 beta chain | A4, A6, A8, A9, AE, AG, AI, AK, AO, AQ, AS, AU, AW, AY, B4, B6, B8, B9, BE, BG, BI, BK, BO, BQ, BS, BU, BW, BY | protein | 49 | Rhodobacter sphaeroides | Q3J1A3 (AlphaFold model) |
| Reaction center protein H chain | AH, BH | protein | 260 | Rhodobacter sphaeroides | P0C0Y7 (AlphaFold model) |
| Reaction center protein L chain | AL, BL | protein | 282 | Rhodobacter sphaeroides | P0C0Y8 |
| Reaction center protein M chain | AM, BM | protein | 308 | Rhodobacter sphaeroides | P0C0Y9 |
Sequence of entity 1 (A1, A2, A3, A5, A7, AD, AF, AJ, AN, AP, AT, AV, AX, AZ, B1, B2, B3, B5, B7, BD, BF, BJ, BN, BP, BT, BV, BX, BZ), FASTA
>4V9G_1 Light-harvesting protein B-875 alpha chain (chains A1, A2, A3, A5, A7, AD, AF, AJ, AN, AP, AT, AV, AX, AZ, B1, B2, B3, B5, B7, BD, BF, BJ, BN, BP, BT, BV, BX, BZ)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 2 (AB, BB), FASTA
>4V9G_2 Intrinsic membrane protein PufX (chains AB, BB)
MADKTIFNDHLNTNPKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQEN
QAPAPNITGALETGIELIKHLV
Sequence of entity 3 (A4, A6, A8, A9, AE, AG, AI, AK, AO, AQ, AS, AU, AW, AY, B4, B6, B8, B9, BE, BG, BI, BK, BO, BQ, BS, BU, BW, BY), FASTA
>4V9G_3 Light-harvesting protein B-875 beta chain (chains A4, A6, A8, A9, AE, AG, AI, AK, AO, AQ, AS, AU, AW, AY, B4, B6, B8, B9, BE, BG, BI, BK, BO, BQ, BS, BU, BW, BY)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 4 (AH, BH), FASTA
>4V9G_4 Reaction center protein H chain (chains AH, BH)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAPKRKSVVAAMLAEYA
Sequence of entity 5 (AL, BL), FASTA
>4V9G_5 Reaction center protein L chain (chains AL, BL)
MALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTW
NPQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPF
AFAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISF
FFTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLS
AVFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 6 (AM, BM), FASTA
>4V9G_6 Reaction center protein M chain (chains AM, BM)
MAEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLS
LFSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIAS
FFMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGI
FSHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIA
DRGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQ
NHGMAPLN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 64 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 4 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 3 |
| PO4 | Phosphate ion | O4 P | 2 |
| FE2 | FE (II) ion | Fe | 2 |
| SPO | Spheroidene | C41 H60 O | 1 |
Primary citation
Three-Dimensional Structure of the Rhodobacter sphaeroides RC-LH1-PufX Complex: Dimerization and Quinone Channels Promoted by PufX. Qian, P., Papiz, M.Z., Jackson, P.J. et al. Biochemistry (2013) 52:7575-7585. DOI 10.1021/bi4011946 · PubMed
Other PDB entries of the same protein (UniProt P0C0X9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9KLM 2.6 Å, Cryo-EM structure of the monomeric Rhodobacter sphaeroides G1C LH1-RC core complex
- 7F0L 2.94 Å, Structure of photosynthetic LH1-rc super-complex of rhodobacter sphaeroides monomer
Browse structure collections
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