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Open data
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Basic information
Entry | Database: PDB / ID: 8q04 | ||||||||||||||||||
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Title | Chlorella sorokiniana Rubisco: D4 symmetry imposed | ||||||||||||||||||
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![]() | PLANT PROTEIN / Rubisco | ||||||||||||||||||
Function / homology | ![]() L-amino acid transmembrane transporter activity / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||||||||||||||
![]() | Barrett, J. / Blaza, J.N. / Mackinder, L.C.M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A promiscuous mechanism to phase separate eukaryotic carbon fixation Authors: Barrett, J. / Naduthodi, M.I.S. / Mao, Y. / Degut, C. / Musial, S. / Leake, M.C. / Plevin, M.J. / McCormick, A.J. / Blaza, J.N. / Mackinder, L.C.M. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 865.1 KB | Display | ![]() |
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PDB format | ![]() | 713.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 107 KB | Display | |
Data in CIF | ![]() | 174.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 18049MC ![]() 8q05C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 52580.418 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: W8SUA8, ribulose-bisphosphate carboxylase #2: Protein | Mass: 20507.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Water | ChemComp-HOH / | |
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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: Rubisco holoenzyme purified from Chlorella sorokiniana UTEX1230 Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Chlorella sorokiniana Rubisco at 0.3 mg/mL (0.5 micromolar) was incubated with alpha3-alpha4 at 16 micromolar. | ||||||||||||||||||||||||||||||
Specimen support | Details: Pressure was not recorded / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 240000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6.52 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4447 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 237035 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: D4 (2x4 fold dihedral) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73962 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 44 / Protocol: FLEXIBLE FIT / Space: REAL Details: Initial rigid body fitting was completed in UCSF Chimrea. Flexible fitting was completed in COOT and the coordinates were real-space refined in Phenix. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |