+Open data
-Basic information
Entry | Database: PDB / ID: 8u66 | |||||||||
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Title | Firmicutes Rubisco | |||||||||
Components | Rubisco | |||||||||
Keywords | LYASE / Carboxylase / Oxygenase | |||||||||
Function / homology | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE Function and homology information | |||||||||
Biological species | Bacillota (low GC Gram+) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å | |||||||||
Authors | Kaeser, B.P. / Liu, A.K. / Shih, P.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Curr Biol / Year: 2023 Title: Deep-branching evolutionary intermediates reveal structural origins of form I rubisco. Authors: Albert K Liu / Benjamin Kaeser / LinXing Chen / Jacob West-Roberts / Leah J Taylor-Kearney / Adi Lavy / Damian Günzing / Wen-Jun Li / Michal Hammel / Eva Nogales / Jillian F Banfield / Patrick M Shih / Abstract: The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life ...The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life assemble as homo-oligomers, the globally predominant form I enzyme-found in plants, algae, and cyanobacteria-forms a unique hetero-oligomeric complex. The recent discovery of a homo-oligomeric sister group to form I rubisco (named form I') has filled a key gap in our understanding of the enigmatic origins of the form I clade. However, to elucidate the series of molecular events leading to the evolution of form I rubisco, we must examine more distantly related sibling clades to contextualize the molecular features distinguishing form I and form I' rubiscos. Here, we present a comparative structural study retracing the evolutionary history of rubisco that reveals a complex structural trajectory leading to the ultimate hetero-oligomerization of the form I clade. We structurally characterize the oligomeric states of deep-branching form Iα and I'' rubiscos recently discovered from metagenomes, which represent key evolutionary intermediates preceding the form I clade. We further solve the structure of form I'' rubisco, revealing the molecular determinants that likely primed the enzyme core for the transition from a homo-oligomer to a hetero-oligomer. Our findings yield new insight into the evolutionary trajectory underpinning the adoption and entrenchment of the prevalent assembly of form I rubisco, providing additional context when viewing the enzyme family through the broader lens of protein evolution. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u66.cif.gz | 686.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u66.ent.gz | 570.9 KB | Display | PDB format |
PDBx/mmJSON format | 8u66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u66_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8u66_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8u66_validation.xml.gz | 99.4 KB | Display | |
Data in CIF | 8u66_validation.cif.gz | 154 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/8u66 ftp://data.pdbj.org/pub/pdb/validation_reports/u6/8u66 | HTTPS FTP |
-Related structure data
Related structure data | 41946MC 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: 50978.855 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillota (low GC Gram+) / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-CAP / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: RUBISCO octamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillota (low GC Gram+) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | |||||||||||||||
Particle selection | Num. of particles selected: 3903212 | |||||||||||||||
3D reconstruction | Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1557723 / Num. of class averages: 2 / Symmetry type: POINT |