8QJ0: PDB entry 8QJ0
Room-temperature Serial Synchrotron Crystallography structure of Spinacia oleracea RuBisCO. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 May 2024.
- Method
- X-ray diffraction
- Resolution
- 2.3 Å
- Organism
- Spinacia oleracea
- Chains
- 8
- Atoms
- 18,884
- Mol. weight
- 270.19 kDa
- Ligands
- MG
- Released
- 29 May 2024
Explore 8QJ0 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8QJ0 contains 130 α-helices and 104 β-strands across 8 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 L: 28 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| β-strand | 25 | 1 | 9 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 9 |
| α-helix | 45 | 1 | |
| α-helix | 50-60 | 11 | |
| α-helix | 70-74 | 5 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-89 | 7 | 9 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 9 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 9 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-162 | 8 | |
| β-strand | 169-173 | 5 | 10 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 10 |
| β-strand | 209 | 1 | 11 |
| β-strand | 212 | 1 | 11 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 10 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 10 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 10 |
| α-helix | 298-302 | 5 | |
| β-strand | 308-309 | 2 | 9 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-327 | 3 | 10 |
| α-helix | 339-350 | 12 | |
| β-strand | 353-354 | 2 | 12 |
| β-strand | 357 | 1 | 13 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 13 |
| β-strand | 366-367 | 2 | 12 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-378 | 4 | 10 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 10 |
| α-helix | 404-407 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-449 | 13 | |
| α-helix | 453-461 | 9 | |
Chains M and O: 28 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| β-strand | 25 | 1 | 14 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 14 |
| α-helix | 45 | 1 | |
| α-helix | 50-60 | 11 | |
| α-helix | 70-74 | 5 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-89 | 7 | 14 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 14 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 14 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-162 | 8 | |
| β-strand | 169-173 | 5 | 15 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 15 |
| β-strand | 209 | 1 | 16 |
| β-strand | 212 | 1 | 16 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 15 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 15 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 15 |
| α-helix | 298-302 | 5 | |
| β-strand | 308-309 | 2 | 14 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-327 | 3 | 15 |
| α-helix | 339-350 | 12 | |
| β-strand | 353-354 | 2 | 17 |
| β-strand | 357 | 1 | 18 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 18 |
| β-strand | 366-367 | 2 | 17 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-378 | 4 | 15 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-401 | 3 | 15 |
| α-helix | 404-407 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-449 | 13 | |
| α-helix | 453-461 | 9 | |
Chain N: 28 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 21-24 | 4 | |
| β-strand | 25 | 1 | 19 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 19 |
| α-helix | 45 | 1 | |
| α-helix | 50-60 | 11 | |
| α-helix | 70-74 | 5 | |
| α-helix | 77-79 | 3 | |
| β-strand | 83-89 | 7 | 19 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 19 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 19 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-162 | 8 | |
| β-strand | 169-173 | 5 | 20 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 20 |
| β-strand | 209 | 1 | 21 |
| β-strand | 212 | 1 | 21 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 20 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 20 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 20 |
| α-helix | 299-302 | 4 | |
| β-strand | 308-309 | 2 | 19 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-327 | 3 | 20 |
| α-helix | 339-350 | 12 | |
| β-strand | 353-354 | 2 | 22 |
| β-strand | 357 | 1 | 23 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 23 |
| β-strand | 366-367 | 2 | 22 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-378 | 4 | 20 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-401 | 3 | 20 |
| α-helix | 404-407 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-449 | 13 | |
| α-helix | 453-461 | 9 | |
Chain S: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 19-22 | 4 | |
| α-helix | 23-35 | 13 | |
| α-helix | 38 | 1 | |
| β-strand | 39-45 | 7 | 1 |
| β-strand | 52 | 1 | 2 |
| β-strand | 63 | 1 | 2 |
| β-strand | 68-70 | 3 | 1 |
| α-helix | 80-93 | 14 | |
| β-strand | 98-105 | 8 | 1 |
| β-strand | 110-118 | 9 | 1 |
Chain T: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 20-22 | 3 | |
| α-helix | 23-35 | 13 | |
| α-helix | 38 | 1 | |
| β-strand | 39-45 | 7 | 3 |
| β-strand | 52 | 1 | 4 |
| β-strand | 63 | 1 | 4 |
| β-strand | 68-70 | 3 | 3 |
| α-helix | 80-93 | 14 | |
| β-strand | 98-105 | 8 | 3 |
| β-strand | 110-118 | 9 | 3 |
Chain U: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 19-22 | 4 | |
| α-helix | 23-35 | 13 | |
| β-strand | 39-45 | 7 | 5 |
| β-strand | 52 | 1 | 6 |
| β-strand | 63 | 1 | 6 |
| β-strand | 68-70 | 3 | 5 |
| α-helix | 80-93 | 14 | |
| β-strand | 98-105 | 8 | 5 |
| β-strand | 110-118 | 9 | 5 |
Chain V: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-5 | 4 | |
| α-helix | 20-22 | 3 | |
| α-helix | 23-35 | 13 | |
| β-strand | 39-45 | 7 | 7 |
| β-strand | 52 | 1 | 8 |
| β-strand | 63 | 1 | 8 |
| β-strand | 68-70 | 3 | 7 |
| α-helix | 80-93 | 14 | |
| β-strand | 98-105 | 8 | 7 |
| β-strand | 110-118 | 9 | 7 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 | S, T, U, V | protein | 123 | Spinacia oleracea | Q43832 (AlphaFold model) |
| Ribulose bisphosphate carboxylase large chain | L, M, N, O | protein | 475 | Spinacia oleracea | P00875 (AlphaFold model) |
Sequence of entity 1 (S, T, U, V), FASTA
>8QJ0_1 Ribulose bisphosphate carboxylase small subunit, chloroplastic 2 (chains S, T, U, V)
MKVWPTQNMKRYETLSYLPPLTTDQLARQVDYLLNNKWVPCLEFETDHGFVYREHHNSPG
YYDGRYWTMWKLPMFGCTDPAQVLNELEECKKEYPNAFIRIIGFDSNRQVQCVSFIAYKP
AGY
Sequence of entity 2 (L, M, N, O), FASTA
>8QJ0_2 Ribulose bisphosphate carboxylase large chain (chains L, M, N, O)
MSPQTETKASVEFKAGVKDYKLTYYTPEYETLDTDILAAFRVSPQPGVPPEEAGAAVAAE
SSTGTWTTVWTDGLTNLDRYKGRCYHIEPVAGEENQYICYVAYPLDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYL
NATAGTCEDMMKRAVFARELGVPIVMHDYLTGGFTANTTLSHYCRDNGLLLHIHRAMHAV
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDYTEKDRSR
GIYFTQSWVSTPGVLPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
RVALEACVQARNEGRDLAREGNTIIREATKWSPELAAACEVWKEIKFEFPAMDTV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
Primary citation
Room-temperature serial synchrotron crystallography structure of Spinacia oleracea RuBisCO. Bjelcic, M., Aurelius, O., Nan, J. et al. Acta Crystallogr F Struct Biol Commun (2024) 80:117-124. DOI 10.1107/S2053230X24004643 · PubMed
Other PDB entries of the same protein (UniProt Q43832 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1IR1 1.8 Å, Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco)…
- 1AA1 2.2 Å, Activated spinach rubisco in complex with the product 3-phosphoglycerate
- 1AUS 2.2 Å, Activated unliganded spinach rubisco
- 1UPM 2.3 Å, Activated spinach rubisco complexed with 2-carboxyarabinitol 2 bisphosphat and CA2+.
- 1UPP 2.3 Å, Spinach rubisco in complex with 2-carboxyarabinitol 2 bisphosphate and calcium.
- 1UZD 2.4 Å, Chlamydomonas,Spinach Chimeric Rubisco
- 9CQ5 2.5 Å, Mn-bound RuBisCO from spinach with CABP inhibitor
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