Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP co-crystallization with spheroidene. Determined by X-ray diffraction at 2.1 Å resolution. Released 2 Dec 2020.
Explore 6Z1J in 3D Show helices and sheets RCSB PDB PDBe
6Z1J contains 51 α-helices and 34 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 | 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 | 5 |
| β-strand | 152-155 | 4 | 5 |
| β-strand | 160-170 | 11 | 5 |
| β-strand | 175-182 | 8 | 5 |
| β-strand | 188-192 | 5 | 5 |
| α-helix | 193-195 | 3 | |
| β-strand | 197-198 | 2 | 5 |
| β-strand | 203-205 | 3 | 5 |
| α-helix | 210-212 | 3 | |
| α-helix | 217-219 | 3 | |
| β-strand | 221 | 1 | 6 |
| β-strand | 224 | 1 | 6 |
| α-helix | 227-243 | 17 | |
| α-helix | 245-247 | 3 |
| 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 | 209-220 | 12 | |
| α-helix | 226-249 | 24 | |
| β-strand | 251 | 1 | 9 |
| β-strand | 255 | 1 | 9 |
| α-helix | 259-262 | 4 | |
| α-helix | 270-273 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 11-13 | 3 | 5 |
| α-helix | 26-28 | 3 | |
| β-strand | 29 | 1 | 10 |
| α-helix | 30-32 | 3 | |
| β-strand | 35 | 1 | 11 |
| α-helix | 37-40 | 4 | |
| β-strand | 46 | 1 | 11 |
| β-strand | 51 | 1 | 10 |
| α-helix | 53-77 | 25 | |
| α-helix | 82-88 | 7 | |
| 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 | 264-285 | 22 | |
| 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 | 241 | 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 | 302 | Rhodobacter sphaeroides | P0C0Y9 (AlphaFold model) |
>6Z1J_1 Reaction center protein H chain (chains H) FDLASLAIYSFWIFLAGLIYYLQTENMREGYPLENEDGTPAANQGPFPLPKPKTFILPHG RGTLTVPGPESEDRPIALARTAVSEGFPHAPTGDPMKDGVGPASWVARRDLPELDGHGHN KIKPMKAAAGFHVSAGKNPIGLPVRGCDLEIAGKVVDIWVDIPEQMARFLEVELKDGSTR LLPMQMVKVQSNRVHVNALSSDLFAGIPTIKSPTEVTLLEEDKICGYVAGGLMYAAPKRK S
>6Z1J_2 Reaction center protein L chain (chains L) ALLSFERKYRVPGGTLVGGNLFDFWVGPFYVGFFGVATFFFAALGIILIAWSAVLQGTWN PQLISVYPPALEYGLGGAPLAKGGLWQIITICATGAFVSWALREVEICRKLGIGYHIPFA FAFAILAYLTLVLFRPVMMGAWGYAFPYGIWTHLDWVSNTGYTYGNFHYNPAHMIAITFF FTNALALALHGALVLSAANPEKGKEMRTPDHEDTFFRDLVGYSIGTLGIHRLGLLLSLSA VFFSALCMIITGTIWFDQWVDWWQWWVKLPWWANIPGGING
>6Z1J_3 Reaction center protein M chain (chains M) AEYQNIFTQVQVRGPADLGMTEDVNLANRSGVGPFSTLLGWFGNAQLGPIYLGSLGVLSL FSGLMWFFTIGIWFWYQAGWNPAVFLRDLFFFSLEPPAPEYGLSFAAPLKEGGLWLIASF FMFVAVWSWWGRTYLRAQALGMGKHTAWAFLSAIWLWMVLGFIRPILMGSWSEAVPYGIF SHLDWTNNFSLVHGNLFYNPFHGLSIAFLYGSALLFAMHGATILAVSRFGGERELEQIAD RGTAAERAALFWRWTMGFNATMEGIHRWAIWMAVLVTLTGGIGILLSGTVVDNWYVWGQN HG
| ID | Name | Formula | Copies |
|---|---|---|---|
| LDA | Lauryl dimethylamine-N-oxide | C14 H31 N O | 4 |
| BCL | Bacteriochlorophyll a | C55 H74 Mg N4 O6 | 4 |
| BPH | Bacteriopheophytin a | C55 H76 N4 O6 | 2 |
| FE | FE (III) ion | Fe | 1 |
| SPN | Speroidenone | C41 H70 O2 | 1 |
| PO4 | Phosphate ion | O4 P | 1 |
| NKP | (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate | C21 H41 O7 P | 2 |
| OLC | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate | C21 H40 O4 | 1 |
| U10 | Ubiquinone-10 | C59 H90 O4 | 1 |
Water and common crystallization additives (UNL) are not listed.
Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center. Selikhanov, G., Fufina, T., Vasilieva, L. et al. IUCrJ (2020) 7:1084-1091. DOI 10.1107/S2052252520012142 · PubMed
Other PDB entries of the same protein (UniProt P0C0Y7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
MolViewer shows 6Z1J 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.