Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1. Determined by X-ray diffraction at 2.01 Å resolution. Released 1 Dec 2010.
Explore 3I4D in 3D Show helices and sheets RCSB PDB PDBe
3I4D contains 52 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 | 12-34 | 23 | |
| 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 |
| α-helix | 134-136 | 3 | |
| β-strand | 141-144 | 4 | 5 |
| β-strand | 152-155 | 4 | 13 |
| β-strand | 160-170 | 11 | 13 |
| β-strand | 175-183 | 9 | 13 |
| β-strand | 188-192 | 5 | 13 |
| α-helix | 193-195 | 3 | |
| β-strand | 197-198 | 2 | 13 |
| β-strand | 203-205 | 3 | 13 |
| α-helix | 210-212 | 3 | |
| α-helix | 217-219 | 3 | |
| α-helix | 227-243 | 17 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2 | 1 | 1 |
| α-helix | 7-9 | 3 | |
| β-strand | 25-26 | 2 | 2 |
| β-strand | 29-30 | 2 | 2 |
| α-helix | 32-56 | 25 | |
| β-strand | 66 | 1 | 3 |
| 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 | 1 | 3 |
| α-helix | 152-162 | 11 | |
| α-helix | 167-169 | 3 | |
| α-helix | 171-198 | 28 | |
| α-helix | 209-220 | 12 | |
| α-helix | 226-249 | 24 | |
| β-strand | 251 | 1 | 4 |
| β-strand | 255 | 1 | 4 |
| α-helix | 259-263 | 5 | |
| α-helix | 264-267 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 11-13 | 3 | 5 |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 6 |
| α-helix | 30-32 | 3 | |
| β-strand | 35 | 1 | 7 |
| α-helix | 37-40 | 4 | |
| β-strand | 46 | 1 | 7 |
| β-strand | 51 | 1 | 6 |
| α-helix | 54-77 | 24 | |
| α-helix | 82-87 | 6 | |
| α-helix | 89-91 | 3 | |
| β-strand | 94 | 1 | 8 |
| α-helix | 96-98 | 3 | |
| α-helix | 99-101 | 3 | |
| α-helix | 109-111 | 3 | |
| α-helix | 113-140 | 28 | |
| 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 | 8 |
| 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 | 264-285 | 22 | |
| β-strand | 287 | 1 | 9 |
| β-strand | 291 | 1 | 9 |
| α-helix | 294-300 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| 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) |
| Reaction center protein H chain | H | protein | 260 | Rhodobacter sphaeroides | P0C0Y7 (AlphaFold model) |
>3I4D_1 Reaction center protein L chain (chains L) ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAISFF FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
>3I4D_2 Reaction center protein M chain (chains M) AEYQNIFSQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN HGMAPLN
>3I4D_3 Reaction center protein H chain (chains H) MVGVTAFGNFDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPK PKTFILPHGRGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDL PELDGHGHNKIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLE VELKDGSTRLLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGG LMYAAPKRKSVVAAMLAEYA
| ID | Name | Formula | Copies |
|---|---|---|---|
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 4 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 2 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 2 |
| UQ1 | Ubiquinone-1 | C14 H18 O4 | 1 |
| PO4 | Phosphate ion | O4 P | 7 |
| DIO | 1,4-diethylene dioxide | C4 H8 O2 | 1 |
| HT3 | (2R,3S)-heptane-1,2,3-triol | C7 H16 O3 | 1 |
| HTO | Heptane-1,2,3-triol | C7 H16 O3 | 2 |
| LDA | Lauryl dimethylamine-N-oxide | C14 H31 N O | 21 |
| 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, K, CL) are not listed.
Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography. Fujii, R., Adachi, S., Roszak, A.W. et al. To be published.
Other PDB entries of the same protein (UniProt P0C0Y8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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