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Open data
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Basic information
Entry | Database: PDB / ID: 7jfo | ||||||||||||||||||||||||||||||
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Title | EPYC1(49-72)-bound Rubisco | ||||||||||||||||||||||||||||||
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![]() | PLANT PROTEIN / Lyase / Rubisco / Pyrenoid | ||||||||||||||||||||||||||||||
Function / homology | ![]() photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast stroma / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.13 Å | ||||||||||||||||||||||||||||||
![]() | Matthies, D. / Jonikas, M.C. / He, S. | ||||||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: The structural basis of Rubisco phase separation in the pyrenoid. Authors: Shan He / Hui-Ting Chou / Doreen Matthies / Tobias Wunder / Moritz T Meyer / Nicky Atkinson / Antonio Martinez-Sanchez / Philip D Jeffrey / Sarah A Port / Weronika Patena / Guanhua He / ...Authors: Shan He / Hui-Ting Chou / Doreen Matthies / Tobias Wunder / Moritz T Meyer / Nicky Atkinson / Antonio Martinez-Sanchez / Philip D Jeffrey / Sarah A Port / Weronika Patena / Guanhua He / Vivian K Chen / Frederick M Hughson / Alistair J McCormick / Oliver Mueller-Cajar / Benjamin D Engel / Zhiheng Yu / Martin C Jonikas / ![]() ![]() ![]() ![]() Abstract: Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO- ...Approximately one-third of global CO fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle. | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 813.2 KB | Display | ![]() |
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PDB format | ![]() | 673.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22308MC ![]() 7jn4C ![]() 7jsxC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.2 TB Data #1: Unaligned multuframe micrographs of EPYC1(49-72) peptide-bound Rubisco [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 52607.812 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00877, ribulose-bisphosphate carboxylase #2: Protein | Mass: 20667.959 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P08475, ribulose-bisphosphate carboxylase #3: Protein/peptide | Mass: 2828.148 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: EPYC1(49-72) peptide-bound Rubisco / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 6.8 Details: 200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: glow discharging for 60 seconds with a current of 15 mA in a Pelico EasiGlow system. Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 58.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2500 |
Image scans | Width: 7676 / Height: 7462 / Movie frames/image: 50 / Used frames/image: 1-50 |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1809869 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 945755 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 1GK8 |