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Yorodumi- PDB-8q05: Chlorella sorokiniana Rubisco with CsLinker (alpha3-alpha4) bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q05 | ||||||||||||||||||
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Title | Chlorella sorokiniana Rubisco with CsLinker (alpha3-alpha4) bound: D4 symmetry expanded | ||||||||||||||||||
Components |
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Keywords | PLANT PROTEIN / Rubisco | ||||||||||||||||||
Function / homology | Function and homology information 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 | Chlorella sorokiniana (plant) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||||||||||||||
Authors | Barrett, J. / Blaza, J.N. / Mackinder, L.C.M. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q05.cif.gz | 869.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q05.ent.gz | 714.6 KB | Display | PDB format |
PDBx/mmJSON format | 8q05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q05_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8q05_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8q05_validation.xml.gz | 109.4 KB | Display | |
Data in CIF | 8q05_validation.cif.gz | 175.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/8q05 ftp://data.pdbj.org/pub/pdb/validation_reports/q0/8q05 | HTTPS FTP |
-Related structure data
Related structure data | 18050MC 8q04C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 14455.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella sorokiniana (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
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#2: Protein | Mass: 52580.418 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlorella sorokiniana (plant) / Strain: UTEX1230 (SAG211-8k) References: UniProt: W8SUA8, ribulose-bisphosphate carboxylase #3: Protein | Mass: 20507.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlorella sorokiniana (plant) / Strain: UTEX1230 (SAG211-8k) / References: UniProt: A0A2P6U2H5 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||||||||||||
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 Rubisco at 0.3 mg/mL (0.5 micromolar) was mixed with the alpha3-alpha4 fragment at 16 micromolar and incubated for 10 minutes at room temperature before grid preparation. | ||||||||||||||||||||||||||||||
Specimen support | Details: The 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 / Details: Blot force -5, 8 s blot |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-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: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133171 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT |