7PQD: LH1-alpha
Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 A: the structural basis for dimerisation. Determined by electron microscopy at 2.9 Å resolution. Released 24 Nov 2021.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organism
- Cereibacter sphaeroides 2.4.1
- Chains
- 70
- Atoms
- 45,952
- Mol. weight
- 676.53 kDa
- Ligands
- BCL, SP2, 3PE, CD4
- Released
- 24 Nov 2021
Explore 7PQD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7PQD contains 244 α-helices and 72 β-strands across 70 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 aa and AA: 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 | 39-41 | 3 | |
Chains ab, AB, ad, AD, af, AF, ai and AI: 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 ac and AC: 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 ae, AE, am and AM: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-6 | 5 | |
| α-helix | 7-10 | 4 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
Chains ag and AG: 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 | |
Chains ah, AH, al and AL: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-9 | 6 | |
| α-helix | 13-36 | 24 | |
| α-helix | 43-50 | 8 | |
Chains aj and AJ: 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 ak and AK: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-9 | 7 | |
| α-helix | 13-37 | 25 | |
| α-helix | 43-50 | 8 | |
9 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 |
|---|
| LH1-alpha | AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an | protein | 58 | Cereibacter sphaeroides 2.4.1 | |
| LH1-beta | BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn | protein | 49 | Cereibacter sphaeroides 2.4.1 | |
| RC-H | H, h | protein | 246 | Cereibacter sphaeroides 2.4.1 | |
| RC-L | L, l | protein | 281 | Cereibacter sphaeroides 2.4.1 | |
| Reaction center protein M chain | M, m | protein | 307 | Cereibacter sphaeroides 2.4.1 | Q3J1A6 (AlphaFold model) |
| PufZ | UA, UB, ua, ub | protein | 31 | Cereibacter sphaeroides 2.4.1 | |
| PufY | UU, uu | protein | 49 | Cereibacter sphaeroides 2.4.1 | |
| PufX | X, x | protein | 55 | Cereibacter sphaeroides 2.4.1 | |
Sequence of entity 1 (AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an), FASTA
>7PQD_1 LH1-alpha (chains AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, aa, ab, ac, ad, ae, af, ag, ah, ai, aj, ak, al, am, an)
MSKFYKIWMIFDPRRVFVAQGVFLFLLAVMIHLILLSTPSYNWLEISAAKYNRVAVAE
Sequence of entity 2 (BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn), FASTA
>7PQD_2 LH1-beta (chains BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, ba, bb, bc, bd, be, bf, bg, bh, bi, bj, bk, bl, bm, bn)
MADKSDLGYTGLTDEQAQELHSVYMSGLWLFSAVAIVAHLAVYIWRPWF
Sequence of entity 3 (H, h), FASTA
>7PQD_3 RC-H (chains H, h)
MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK
PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL
PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE
VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG
LMYAAP
Sequence of entity 4 (L, l), FASTA
>7PQD_4 RC-L (chains L, l)
ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN
PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA
FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFF
FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA
VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
Sequence of entity 5 (M, m), FASTA
>7PQD_5 Reaction center protein M chain (chains M, m)
AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL
FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF
FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF
SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD
RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN
HGMAPLN
Sequence of entity 6 (UA, UB, ua, ub), FASTA
>7PQD_6 PufZ (chains UA, UB, ua, ub)
MAYMFGIIVFLAMLAVCWFGFMAAERQAGRL
Sequence of entity 7 (UU, uu), FASTA
>7PQD_7 PufY (chains UU, uu)
EVSEFAFRLMMAAVIFVGVGIMFAFAGGHWFVGLVVGGLVAAFFAATPN
Sequence of entity 8 (X, x), FASTA
>7PQD_8 PufX (chains X, x)
PKTNLRLWVAFQMMKGAGWAGGVFFGTLLLIGFFRVVGRMLPIQENQAPAPNITG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 64 |
| SP2 | 3,4-dihydrospheroidene | C41 H62 O | 54 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | C41 H82 N O8 P | 4 |
| CD4 | (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy… | C65 H126 O17 P2 | 4 |
| UQ1 | Ubiquinone-1 | C14 H18 O4 | 2 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 4 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 4 |
| SQD | 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-alpha-D-glucopyranosyl]-sn-glycerol | C41 H78 O12 S | 2 |
| LMT | Dodecyl-beta-D-maltoside | C24 H46 O11 | 2 |
| FE | FE (III) ion | Fe | 2 |
Primary citation
Cryo-EM structure of the dimeric Rhodobacter sphaeroides RC-LH1 core complex at 2.9 angstrom : the structural basis for dimerisation. Qian, P., Croll, T.I., Hitchcock, A. et al. Biochem J (2021) 478:3923-3937. DOI 10.1042/BCJ20210696 · PubMed
Other PDB entries of the same protein (UniProt Q3J1A6 (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
About this viewer
MolViewer shows 7PQD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.