X-ray high resolution structure of the photosynthetic reaction center from Rb. sphaeroides at pH 8 in the charge-separated state. Determined by X-ray diffraction at 2.07 Å resolution. Released 3 Jul 2007.
Explore 2J8D in 3D Show helices and sheets RCSB PDB PDBe
2J8D contains 53 α-helices and 32 β-strands across 3 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 11-34 | 24 | |
| β-strand | 43 | 1 | 1 |
| β-strand | 49 | 1 | 1 |
| α-helix | 50 | 1 | |
| α-helix | 56-61 | 6 | |
| β-strand | 62-66 | 5 | 2 |
| β-strand | 71-75 | 5 | 2 |
| β-strand | 87-89 | 3 | 3 |
| β-strand | 98-100 | 3 | 3 |
| α-helix | 104-107 | 4 | |
| α-helix | 110-112 | 3 | |
| β-strand | 123 | 1 | 4 |
| β-strand | 129 | 1 | 4 |
| β-strand | 131-133 | 3 | 5 |
| α-helix | 134-136 | 3 | |
| β-strand | 141-144 | 4 | 6 |
| β-strand | 152-154 | 3 | 5 |
| β-strand | 160-170 | 11 | 5 |
| β-strand | 175-183 | 9 | 5 |
| β-strand | 188-192 | 5 | 5 |
| α-helix | 193-195 | 3 | |
| β-strand | 197-198 | 2 | 5 |
| β-strand | 203-204 | 2 | 5 |
| α-helix | 210-212 | 3 | |
| α-helix | 217-219 | 3 | |
| α-helix | 227-243 | 17 | |
| α-helix | 245-249 | 5 | |
| α-helix | 251-254 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2 | 1 | 1 |
| α-helix | 7-9 | 3 | |
| β-strand | 25-26 | 2 | 7 |
| β-strand | 29-30 | 2 | 7 |
| α-helix | 32-56 | 25 | |
| β-strand | 65-66 | 2 | 8 |
| α-helix | 67-70 | 4 | |
| α-helix | 71-73 | 3 | |
| α-helix | 80-82 | 3 | |
| α-helix | 84-111 | 28 | |
| α-helix | 116-129 | 14 | |
| α-helix | 130-134 | 5 | |
| α-helix | 135-139 | 5 | |
| α-helix | 142-144 | 3 | |
| α-helix | 146-147 | 2 | |
| β-strand | 148-149 | 2 | 8 |
| α-helix | 152-162 | 11 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-198 | 28 | |
| α-helix | 204-207 | 4 | |
| α-helix | 209-220 | 12 | |
| α-helix | 225-249 | 25 | |
| β-strand | 251 | 1 | 9 |
| β-strand | 255 | 1 | 9 |
| α-helix | 259-262 | 4 | |
| α-helix | 264-267 | 4 | |
| α-helix | 270-273 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 11-13 | 3 | 6 |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 10 |
| β-strand | 35 | 1 | 11 |
| α-helix | 39-41 | 3 | |
| β-strand | 46 | 1 | 11 |
| β-strand | 51 | 1 | 10 |
| α-helix | 53-77 | 25 | |
| α-helix | 82-87 | 6 | |
| β-strand | 94 | 1 | 12 |
| α-helix | 95-98 | 4 | |
| α-helix | 99-101 | 3 | |
| α-helix | 109-111 | 3 | |
| α-helix | 113-139 | 27 | |
| α-helix | 145-158 | 14 | |
| α-helix | 159-163 | 5 | |
| α-helix | 164-168 | 5 | |
| α-helix | 171-173 | 3 | |
| α-helix | 175-176 | 2 | |
| β-strand | 177 | 1 | 12 |
| α-helix | 179-192 | 14 | |
| α-helix | 196-198 | 3 | |
| α-helix | 200-225 | 26 | |
| α-helix | 227-229 | 3 | |
| α-helix | 234-239 | 6 | |
| α-helix | 243-256 | 14 | |
| α-helix | 262-286 | 25 | |
| β-strand | 287 | 1 | 13 |
| β-strand | 291 | 1 | 13 |
| α-helix | 294-300 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Reaction center protein H chain | H | protein | 260 | RHODOBACTER SPHAEROIDES | P0C0Y7 (AlphaFold model) |
| Reaction center protein L chain | L | protein | 281 | RHODOBACTER SPHAEROIDES | P0C0Y8 (AlphaFold model) |
| Reaction center protein M chain | M | protein | 307 | RHODOBACTER SPHAEROIDES | P0C0Y9 (AlphaFold model) |
>2J8D_1 REACTION CENTER PROTEIN H CHAIN (chains H) MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG LMYAAPKRKSVVAAMLAEYA
>2J8D_2 REACTION CENTER PROTEIN L CHAIN (chains L) ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFF FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
>2J8D_3 REACTION CENTER PROTEIN M CHAIN (chains M) AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN HGMAPLN
| ID | Name | Formula | Copies |
|---|---|---|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 4 |
| LDA | Lauryl dimethylamine-N-oxide | C14 H31 N O | 9 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 2 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 2 |
| PO4 | Phosphate ion | O4 P | 1 |
| HTO | Heptane-1,2,3-triol | C7 H16 O3 | 2 |
| FE | FE (III) ion | Fe | 1 |
| SPO | Spheroidene | C41 H60 O | 1 |
| CDL | Cardiolipin | C81 H156 O17 P2 | 1 |
Water and common crystallization additives (GOL) are not listed.
Ph Modulates the Quinone Position in the Photosynthetic Reaction Center from Rhodobacter Sphaeroides in the Neutral and Charge Separated States. Koepke, J., Krammer, E.M., Klingen, A.R. et al. J Mol Biol (2007) 371:396. DOI 10.1016/J.JMB.2007.04.082 · PubMed
Other PDB entries of the same protein (UniProt P0C0Y7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 2J8D 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.