+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41946 | |||||||||
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Title | Firmicutes Rubisco | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Carboxylase / Oxygenase / LYASE | |||||||||
Biological species | Bacillota (low GC Gram+) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.21 Å | |||||||||
Authors | Kaeser BP / Liu AK / Shih PM | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41946.map.gz | 97.1 MB | EMDB map data format | |
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Header (meta data) | emd-41946-v30.xml emd-41946.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41946_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_41946.png | 39.6 KB | ||
Filedesc metadata | emd-41946.cif.gz | 5.7 KB | ||
Others | emd_41946_half_map_1.map.gz emd_41946_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41946 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41946 | HTTPS FTP |
-Validation report
Summary document | emd_41946_validation.pdf.gz | 924 KB | Display | EMDB validaton report |
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Full document | emd_41946_full_validation.pdf.gz | 923.6 KB | Display | |
Data in XML | emd_41946_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_41946_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41946 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41946 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41946.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41946_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41946_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RUBISCO octamer
Entire | Name: RUBISCO octamer |
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Components |
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-Supramolecule #1: RUBISCO octamer
Supramolecule | Name: RUBISCO octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillota (low GC Gram+) |
-Macromolecule #1: Rubisco
Macromolecule | Name: Rubisco / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillota (low GC Gram+) |
Molecular weight | Theoretical: 50.978855 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MARQQFVAGV QPYRKTYYEP GYEPKETDLL CAFRIEPSPG IPLEEAAAAV AAESSTGTWT EVWSQEMTDL HRYKGRCYAI DGNTAYIAY PLDLFEEGSI VNVMSSIVGN VFGFKAVRAL RLLDMRIPTA YLKTFPGPPT GIAQERDRLK VYHRPLLGGT I KPKLGLGP ...String: MARQQFVAGV QPYRKTYYEP GYEPKETDLL CAFRIEPSPG IPLEEAAAAV AAESSTGTWT EVWSQEMTDL HRYKGRCYAI DGNTAYIAY PLDLFEEGSI VNVMSSIVGN VFGFKAVRAL RLLDMRIPTA YLKTFPGPPT GIAQERDRLK VYHRPLLGGT I KPKLGLGP KEFARVVYEC LVGGLDTT(KCX)D DENLNSQPFC RWRDRYLYVM DAVHRAEEET GEAKGHWLNV TAGDTEEM L RRAEFAKEVG SRYIMVDFLT AGFSAYATLR RRAEELGLMI HCHRAMHAVF TRPKDHGIHF RVVAKWLRMA GGDHVHTGT VVGKLEGARE EVRGIADLLR EEFVPANPQR GLLFDQPWAG LKPLFPVASG GIHVWHVPDL VSIYGNDAFF LFGGGTHGHP RGSRAGARA NRAAVEAVAA AYREGRDILA EGRQILQDAA RTCPELREAM ELWEGVTFGE E |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Macromolecule | Name: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: CAP |
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Molecular weight | Theoretical: 356.115 Da |
Chemical component information | ChemComp-CAP: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 981 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |