7PIL: Light-harvesting protein B-875 alpha chain
Cryo-EM structure of the Rhodobacter sphaeroides RC-LH1-PufXY monomer complex at 2.5 A. Determined by electron microscopy at 2.5 Å resolution. Released 13 Oct 2021.
- Method
- Electron microscopy
- Resolution
- 2.5 Å
- Organisms
- Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.), Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
- Chains
- 33
- Atoms
- 22,480
- Mol. weight
- 317.89 kDa
- Ligands
- SPO, BCL, FE, CD4
- Released
- 13 Oct 2021
Explore 7PIL in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7PIL contains 119 α-helices and 38 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.
Chain AA: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-36 | 24 | |
Chains AB, AC and AK: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-36 | 24 | |
| α-helix | 43-50 | 8 | |
Chain AD: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-6 | 3 | |
| α-helix | 7-10 | 4 | |
| α-helix | 13-36 | 24 | |
| α-helix | 43-50 | 8 | |
Chains AE, AJ and AL: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 7-10 | 4 | |
| α-helix | 13-36 | 24 | |
| α-helix | 43-50 | 8 | |
Chains AF, AG and AH: 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 AI: 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 AM: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-9 | 8 | |
| α-helix | 13-36 | 24 | |
| α-helix | 43-50 | 8 | |
Chain AN: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-36 | 24 | |
| 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 |
|---|
| Light-harvesting protein B-875 alpha chain | AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN | protein | 55 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | Q3J1A4 (AlphaFold model) |
| Light-harvesting protein B-875 beta chain | BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN | protein | 43 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | Q3J1A3 (AlphaFold model) |
| Reaction center protein H chain | H | protein | 246 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | Q3J170 (AlphaFold model) |
| Reaction center protein L chain | L | protein | 281 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | Q3J1A5 (AlphaFold model) |
| Reaction center protein M chain | M | protein | 307 | Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158) | Q3J1A6 |
| RC-Y | UU | protein | 49 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | U5NME9 |
| Intrinsic membrane protein PufX | X | protein | 55 | Rhodobacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) | P13402 |
Sequence of entity 1 (AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN), FASTA
>7PIL_1 Light-harvesting protein B-875 alpha chain (chains AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVA
Sequence of entity 2 (BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN), FASTA
>7PIL_2 Light-harvesting protein B-875 beta chain (chains BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN)
LGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 3 (H), FASTA
>7PIL_3 Reaction center protein H chain (chains H)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAP
Sequence of entity 4 (L), FASTA
>7PIL_4 Reaction center protein L chain (chains L)
ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFF
FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 5 (M), FASTA
>7PIL_5 Reaction center protein M chain (chains M)
AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL
FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF
FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF
SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD
RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN
HGMAPLN
Sequence of entity 6 (UU), FASTA
>7PIL_6 RC-Y (chains UU)
EVSEFAFRLMMAAVIFVGVGIMFAFAGGHWFVGLVVGGLVAAFFAATPN
Sequence of entity 7 (X), FASTA
>7PIL_7 Intrinsic membrane protein PufX (chains X)
PKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGLMLPIQENQAPAPNITG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SPO | Spheroidene | C41 H60 O | 26 |
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 32 |
| FE | FE (III) ion | Fe | 1 |
| CD4 | (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy… | C65 H126 O17 P2 | 1 |
| UQ1 | Ubiquinone-1 | C14 H18 O4 | 1 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 2 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 2 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 4 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 4 |
Primary citation
Cryo-EM structure of the monomeric Rhodobacter sphaeroides RC-LH1 core complex at 2.5 angstrom. Qian, P., Swainsbury, D.J.K., Croll, T.I. et al. Biochem J (2021) 478:3775-3790. DOI 10.1042/BCJ20210631 · PubMed
Other PDB entries of the same protein (UniProt Q3J1A4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 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
- 7VOY 4.2 Å, Rba sphaeroides PufX-KO RC-LH1
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