9HVM: In-cell Structure of Pyrenoid Rubisco
In-cell Structure of Pyrenoid Rubisco. Determined by electron microscopy at 8.1 Å resolution. Released 5 Mar 2025.
- Method
- Electron microscopy
- Resolution
- 8.1 Å
- Organism
- Chlamydomonas reinhardtii
- Chains
- 16
- Atoms
- 37,816
- Mol. weight
- 538.49 kDa
- Released
- 5 Mar 2025
Explore 9HVM in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9HVM contains 224 α-helices and 195 β-strands across 16 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 A: 24 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 20-22 | 3 | |
| β-strand | 25 | 1 | 1 |
| β-strand | 36-44 | 9 | 1 |
| α-helix | 50-62 | 13 | |
| α-helix | 70-74 | 5 | |
| β-strand | 83-84 | 2 | 1 |
| β-strand | 88-89 | 2 | 1 |
| β-strand | 97-103 | 7 | 1 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 118-122 | 5 | |
| β-strand | 130-139 | 10 | 1 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-161 | 7 | |
| β-strand | 169-173 | 5 | 2 |
| α-helix | 182-195 | 14 | |
| β-strand | 199-201 | 3 | 2 |
| α-helix | 204-207 | 4 | |
| α-helix | 214-230 | 17 | |
| β-strand | 237-239 | 3 | 2 |
| β-strand | 240-241 | 2 | 3 |
| α-helix | 247-258 | 12 | |
| β-strand | 265-267 | 3 | 3 |
| α-helix | 269-272 | 4 | |
| β-strand | 273 | 1 | 4 |
| α-helix | 274-286 | 13 | |
| β-strand | 291-293 | 3 | 3 |
| α-helix | 311-319 | 9 | |
| β-strand | 325-326 | 2 | 3 |
| α-helix | 339-350 | 12 | |
| α-helix | 358-360 | 3 | |
| β-strand | 375-376 | 2 | 3 |
| α-helix | 377 | 1 | |
| β-strand | 378 | 1 | 2 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 2 |
| α-helix | 413-432 | 20 | |
| α-helix | 437-448 | 12 | |
| α-helix | 453-461 | 9 | |
Chains B, D, J and P: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 68-80 | 13 | |
| β-strand | 84-91 | 8 | 5 |
| β-strand | 98 | 1 | 6 |
| α-helix | 100-103 | 4 | |
| β-strand | 114 | 1 | 6 |
| β-strand | 119-124 | 6 | 5 |
| α-helix | 131-144 | 14 | |
| β-strand | 148-156 | 9 | 5 |
| β-strand | 161-164 | 4 | 5 |
| β-strand | 169 | 1 | 5 |
Chain C: 25 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 20-22 | 3 | |
| β-strand | 25 | 1 | 7 |
| β-strand | 36-44 | 9 | 7 |
| α-helix | 45 | 1 | |
| α-helix | 50-62 | 13 | |
| α-helix | 70-74 | 5 | |
| β-strand | 83-84 | 2 | 7 |
| β-strand | 88-89 | 2 | 7 |
| β-strand | 97-103 | 7 | 7 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 118-122 | 5 | |
| β-strand | 130-139 | 10 | 7 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-161 | 7 | |
| β-strand | 169-173 | 5 | 8 |
| α-helix | 182-195 | 14 | |
| β-strand | 199-201 | 3 | 8 |
| α-helix | 204-207 | 4 | |
| α-helix | 214-230 | 17 | |
| β-strand | 237-239 | 3 | 8 |
| α-helix | 247-258 | 12 | |
| β-strand | 265-267 | 3 | 9 |
| α-helix | 269-272 | 4 | |
| β-strand | 273 | 1 | 10 |
| α-helix | 274-286 | 13 | |
| β-strand | 291-293 | 3 | 9 |
| α-helix | 311-319 | 9 | |
| β-strand | 325-326 | 2 | 9 |
| α-helix | 339-350 | 12 | |
| α-helix | 358-360 | 3 | |
| β-strand | 375-376 | 2 | 9 |
| α-helix | 377 | 1 | |
| β-strand | 378 | 1 | 8 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 8 |
| α-helix | 413-432 | 20 | |
| α-helix | 437-448 | 12 | |
| α-helix | 453-461 | 9 | |
Chain E: 24 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| β-strand | 16 | 1 | 13 |
| α-helix | 20-22 | 3 | |
| β-strand | 25 | 1 | 14 |
| β-strand | 36-44 | 9 | 14 |
| α-helix | 45 | 1 | |
| α-helix | 50-62 | 13 | |
| β-strand | 68 | 1 | 13 |
| α-helix | 70-74 | 5 | |
| β-strand | 83-84 | 2 | 14 |
| β-strand | 88-89 | 2 | 14 |
| β-strand | 97-103 | 7 | 14 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 118-122 | 5 | |
| β-strand | 130-139 | 10 | 14 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-161 | 7 | |
| β-strand | 169-173 | 5 | 15 |
| α-helix | 182-195 | 14 | |
| β-strand | 199-201 | 3 | 15 |
| α-helix | 204-207 | 4 | |
| α-helix | 214-230 | 17 | |
| β-strand | 237-239 | 3 | 15 |
| β-strand | 240 | 1 | 16 |
| α-helix | 247-258 | 12 | |
| β-strand | 265-267 | 3 | 16 |
| α-helix | 269-272 | 4 | |
| β-strand | 273 | 1 | 17 |
| α-helix | 274-287 | 14 | |
| β-strand | 291-293 | 3 | 16 |
| α-helix | 311-319 | 9 | |
| β-strand | 325-327 | 3 | 16 |
| α-helix | 339-350 | 12 | |
| α-helix | 358-360 | 3 | |
| β-strand | 375-377 | 3 | 16 |
| β-strand | 378 | 1 | 15 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 15 |
| α-helix | 413-432 | 20 | |
| α-helix | 437-448 | 12 | |
| α-helix | 453-461 | 9 | |
Chain F: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 68-80 | 13 | |
| β-strand | 84-91 | 8 | 18 |
| α-helix | 92-94 | 3 | |
| β-strand | 98 | 1 | 19 |
| α-helix | 100-103 | 4 | |
| β-strand | 114 | 1 | 19 |
| β-strand | 119-124 | 6 | 18 |
| α-helix | 131-144 | 14 | |
| β-strand | 148-156 | 9 | 18 |
| β-strand | 161-164 | 4 | 18 |
| β-strand | 169 | 1 | 18 |
Chain G: 24 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| α-helix | 17-19 | 3 | |
| α-helix | 20-22 | 3 | |
| β-strand | 25 | 1 | 20 |
| β-strand | 36-44 | 9 | 20 |
| α-helix | 50-62 | 13 | |
| α-helix | 70-74 | 5 | |
| β-strand | 83-84 | 2 | 20 |
| β-strand | 88-89 | 2 | 20 |
| β-strand | 97-103 | 7 | 20 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 118-122 | 5 | |
| β-strand | 130-139 | 10 | 20 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-161 | 7 | |
| β-strand | 169-173 | 5 | 21 |
| α-helix | 182-195 | 14 | |
| β-strand | 199-201 | 3 | 21 |
| α-helix | 204-207 | 4 | |
| α-helix | 214-230 | 17 | |
| β-strand | 237-239 | 3 | 21 |
| α-helix | 247-258 | 12 | |
| β-strand | 265-267 | 3 | 22 |
| α-helix | 269-272 | 4 | |
| β-strand | 273 | 1 | 17 |
| α-helix | 274-286 | 13 | |
| β-strand | 291-293 | 3 | 22 |
| α-helix | 311-319 | 9 | |
| β-strand | 325-327 | 3 | 22 |
| α-helix | 339-350 | 12 | |
| α-helix | 358-360 | 3 | |
| β-strand | 375-377 | 3 | 22 |
| β-strand | 378 | 1 | 21 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 21 |
| α-helix | 413-432 | 20 | |
| α-helix | 437-448 | 12 | |
| α-helix | 453-461 | 9 | |
Chain H: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 64-67 | 4 | |
| α-helix | 68-80 | 13 | |
| β-strand | 84-91 | 8 | 23 |
| β-strand | 98 | 1 | 24 |
| α-helix | 100-103 | 4 | |
| β-strand | 114 | 1 | 24 |
| β-strand | 119-120 | 2 | 23 |
| α-helix | 131-144 | 14 | |
| β-strand | 148-156 | 9 | 23 |
| β-strand | 161-164 | 4 | 23 |
| β-strand | 169 | 1 | 23 |
Chain I: 24 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-14 | 2 | |
| β-strand | 16 | 1 | 25 |
| α-helix | 20-22 | 3 | |
| β-strand | 25 | 1 | 26 |
| β-strand | 36-44 | 9 | 26 |
| α-helix | 45 | 1 | |
| α-helix | 50-62 | 13 | |
| β-strand | 68 | 1 | 25 |
| α-helix | 70-74 | 5 | |
| β-strand | 83-84 | 2 | 26 |
| β-strand | 88-89 | 2 | 26 |
| β-strand | 97-103 | 7 | 26 |
| α-helix | 105-107 | 3 | |
| α-helix | 113-117 | 5 | |
| α-helix | 118-122 | 5 | |
| β-strand | 130-139 | 10 | 26 |
| α-helix | 142-145 | 4 | |
| α-helix | 155-161 | 7 | |
| β-strand | 169-173 | 5 | 27 |
| α-helix | 182-195 | 14 | |
| β-strand | 199-201 | 3 | 27 |
| α-helix | 204-207 | 4 | |
| α-helix | 214-230 | 17 | |
| β-strand | 237-239 | 3 | 27 |
| α-helix | 247-258 | 12 | |
| β-strand | 265-267 | 3 | 28 |
| α-helix | 269-272 | 4 | |
| β-strand | 273 | 1 | 10 |
| α-helix | 274-287 | 14 | |
| β-strand | 291-293 | 3 | 28 |
| α-helix | 311-319 | 9 | |
| β-strand | 325-327 | 3 | 28 |
| α-helix | 339-350 | 12 | |
| α-helix | 358-360 | 3 | |
| β-strand | 375-377 | 3 | 28 |
| β-strand | 378 | 1 | 27 |
| α-helix | 384-386 | 3 | |
| α-helix | 387-394 | 8 | |
| β-strand | 399-402 | 4 | 27 |
| α-helix | 413-432 | 20 | |
| α-helix | 437-448 | 12 | |
| α-helix | 453-461 | 9 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Ribulose bisphosphate carboxylase large chain | A, C, E, G, I, K, M, O | protein | 469 | Chlamydomonas reinhardtii | P00877 (AlphaFold model) |
| Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 | B, D, F, H, J, L, N, P | protein | 132 | Chlamydomonas reinhardtii | P00873 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA
>9HVM_1 Ribulose bisphosphate carboxylase large chain (chains A, C, E, G, I, K, M, O)
TKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQLGVPPEECGAAVAAESSTGTW
TTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSIVGNVFG
FKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYG
RAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGT
CEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAVIDRQRN
HGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSRGIYFTQ
DWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAANRVALEA
CTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL
Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA
>9HVM_2 Ribulose bisphosphate carboxylase small subunit, chloroplastic 1 (chains B, D, F, H, J, L, N, P)
MMVWTPVNNKMFETFSYLPPLTDEQIAAQVDYIVANGWIPCLEFAEADKAYVSNESAIRF
GSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMG
FLVQRPKTARDF
Primary citation
In-cell structure and variability of pyrenoid Rubisco. Elad, N., Hou, Z., Dumoux, M. et al. Nat Commun (2025) 16:7763-7763. DOI 10.1038/s41467-025-62998-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
- 7JSX 2.06 Å, EPYC1(106-135) peptide-bound Rubisco
- 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…
Browse structure collections
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