7JSX: EPYC1(106-135) peptide-bound Rubisco
EPYC1(106-135) peptide-bound Rubisco. Determined by electron microscopy at 2.06 Å resolution. Released 18 Nov 2020.
- Method
- Electron microscopy
- Resolution
- 2.06 Å
- Organism
- Chlamydomonas reinhardtii
- Chains
- 24
- Atoms
- 38,813
- Mol. weight
- 612.56 kDa
- Released
- 18 Nov 2020
Explore 7JSX in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7JSX contains 248 α-helices and 208 β-strands across 24 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 A and E: 24 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25 | 1 | 1 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 1 |
| α-helix | 45 | 1 | |
| α-helix | 50-59 | 10 | |
| β-strand | 83-89 | 7 | 1 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 1 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 1 |
| α-helix | 142-145 | 4 | |
| α-helix | 154-162 | 9 | |
| β-strand | 169-173 | 5 | 2 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 2 |
| β-strand | 209 | 1 | 3 |
| β-strand | 212 | 1 | 3 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 2 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 2 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 2 |
| α-helix | 298-302 | 5 | |
| β-strand | 308-309 | 2 | 1 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-327 | 3 | 2 |
| α-helix | 336-350 | 15 | |
| β-strand | 353-354 | 2 | 4 |
| β-strand | 357 | 1 | 5 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 5 |
| β-strand | 366-367 | 2 | 4 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-379 | 5 | 2 |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 2 |
| α-helix | 405-408 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-451 | 15 | |
| α-helix | 453-460 | 8 | |
Chains B, F, H, L and N: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 23-35 | 13 | |
| β-strand | 39-46 | 8 | 6 |
| α-helix | 47-50 | 4 | |
| β-strand | 53 | 1 | 7 |
| α-helix | 55-59 | 5 | |
| β-strand | 69 | 1 | 7 |
| β-strand | 74-76 | 3 | 6 |
| α-helix | 86-99 | 14 | |
| β-strand | 103-111 | 9 | 6 |
| β-strand | 116-124 | 9 | 6 |
Chains C, I, K, M and O: 24 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25 | 1 | 8 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 8 |
| α-helix | 45 | 1 | |
| α-helix | 50-59 | 10 | |
| β-strand | 83-89 | 7 | 8 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 8 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 8 |
| α-helix | 142-145 | 4 | |
| α-helix | 154-162 | 9 | |
| β-strand | 169-173 | 5 | 9 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 9 |
| β-strand | 209 | 1 | 10 |
| β-strand | 212 | 1 | 10 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 9 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 9 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 9 |
| α-helix | 298-302 | 5 | |
| β-strand | 308-309 | 2 | 8 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-330 | 6 | 9 |
| α-helix | 336-350 | 15 | |
| β-strand | 353-354 | 2 | 11 |
| β-strand | 357 | 1 | 12 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 12 |
| β-strand | 366-367 | 2 | 11 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-379 | 5 | 9 |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 9 |
| α-helix | 405-408 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-451 | 15 | |
| α-helix | 453-460 | 8 | |
Chains D, J and P: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-22 | 4 | |
| α-helix | 23-35 | 13 | |
| β-strand | 39-46 | 8 | 13 |
| α-helix | 47-49 | 3 | |
| β-strand | 53 | 1 | 14 |
| α-helix | 55-59 | 5 | |
| β-strand | 69 | 1 | 14 |
| β-strand | 74-76 | 3 | 13 |
| α-helix | 86-99 | 14 | |
| β-strand | 103-111 | 9 | 13 |
| β-strand | 116-124 | 9 | 13 |
Chain G: 24 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 25 | 1 | 22 |
| α-helix | 29-32 | 4 | |
| β-strand | 36-44 | 9 | 22 |
| α-helix | 45 | 1 | |
| α-helix | 50-59 | 10 | |
| β-strand | 83-89 | 7 | 22 |
| α-helix | 90 | 1 | |
| β-strand | 97-103 | 7 | 22 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-121 | 9 | |
| α-helix | 124-126 | 3 | |
| β-strand | 130-139 | 10 | 22 |
| α-helix | 142-145 | 4 | |
| α-helix | 154-162 | 9 | |
| β-strand | 169-173 | 5 | 23 |
| α-helix | 182-194 | 13 | |
| β-strand | 199-201 | 3 | 23 |
| β-strand | 209 | 1 | 24 |
| β-strand | 212 | 1 | 24 |
| α-helix | 214-232 | 19 | |
| β-strand | 237-241 | 5 | 23 |
| α-helix | 247-260 | 14 | |
| β-strand | 264-268 | 5 | 23 |
| α-helix | 269-272 | 4 | |
| α-helix | 274-287 | 14 | |
| β-strand | 290-294 | 5 | 23 |
| α-helix | 298-302 | 5 | |
| β-strand | 308-309 | 2 | 22 |
| α-helix | 311-321 | 11 | |
| β-strand | 325-327 | 3 | 23 |
| α-helix | 336-350 | 15 | |
| β-strand | 353-354 | 2 | 25 |
| β-strand | 357 | 1 | 26 |
| α-helix | 358-360 | 3 | |
| β-strand | 362 | 1 | 26 |
| β-strand | 366-367 | 2 | 25 |
| α-helix | 371-373 | 3 | |
| β-strand | 375-380 | 6 | 23 |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 23 |
| α-helix | 405-408 | 4 | |
| α-helix | 413-432 | 20 | |
| α-helix | 437-451 | 15 | |
| α-helix | 453-460 | 8 | |
Chains q, r, s, t, u, v, w and x: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 121-123 | 3 | |
| α-helix | 126-134 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ribulose bisphosphate carboxylase large chain | A, C, E, G, I, K, M, O | protein | 475 | Chlamydomonas reinhardtii | P00877 (AlphaFold model) |
| Ribulose bisphosphate carboxylase small chain 2, chloroplastic | B, D, F, H, J, L, N, P | protein | 185 | Chlamydomonas reinhardtii | P08475 (AlphaFold model) |
| EPYC1 | q, r, s, t, u, v, w, x | protein | 30 | Chlamydomonas reinhardtii | A0A2K3DA85 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA
>7JSX_1 Ribulose bisphosphate carboxylase large chain (chains A, C, E, G, I, K, M, O)
MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAE
SSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSI
VGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGL
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYL
NATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAV
IDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSR
GIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAAN
RVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL
Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA
>7JSX_2 Ribulose bisphosphate carboxylase small chain 2, chloroplastic (chains B, D, F, H, J, L, N, P)
MAAVIAKSSVSAAVARPARSSVRPMAALKPAVKAAPVAAPAQANQMMVWTPVNNKMFETF
SYLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVSNESAIRFGSVSCLYYDNRYWTM
WKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKSARDWQPA
NKRSV
Sequence of entity 3 (q, r, s, t, u, v, w, x), FASTA
>7JSX_3 EPYC1 (chains q, r, s, t, u, v, w, x)
RSSSASKKAVTPSRSALPSNWKQELESLRS
Primary citation
The structural basis of Rubisco phase separation in the pyrenoid. He, S., Chou, H.T., Matthies, D. et al. Nat Plants (2020) 6:1480-1490. DOI 10.1038/s41477-020-00811-y · PubMed
Other PDB entries of the same protein (UniProt P00877 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1GK8 1.4 Å, Rubisco from Chlamydomonas reinhardtii
- 2V6A 1.5 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations…
- 2V63 1.8 Å, Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A…
- 1IR2 1.84 Å, Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco)…
- 5BS2 1.97 Å, Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL…
- 2V67 2.0 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit supressor…
- 1UW9 2.05 Å, L290F-A222T chlamydomonas Rubisco mutant
- 7JFO 2.13 Å, EPYC1(49-72)-bound Rubisco
- 1UZH 2.2 Å, A chimeric chlamydomonas, synechococcus rubisco enzyme
- 1UWA 2.3 Å, L290F mutant rubisco from chlamydomonas
- 2V68 2.3 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations…
- 2VDH 2.3 Å, Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit C172S…
Browse structure collections
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