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Yorodumi- EMDB-14178: Fiber-forming RubisCO derived from ancestral sequence reconstruct... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14178 | |||||||||
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Title | Fiber-forming RubisCO derived from ancestral sequence reconstruction and rational engineering | |||||||||
Map data | ||||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Schulz L / Zarzycki J / Prinz S / Schuller JM / Erb TJ / Hochberg GKA | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Science / Year: 2022 Title: Evolution of increased complexity and specificity at the dawn of form I Rubiscos. Authors: Luca Schulz / Zhijun Guo / Jan Zarzycki / Wieland Steinchen / Jan M Schuller / Thomas Heimerl / Simone Prinz / Oliver Mueller-Cajar / Tobias J Erb / Georg K A Hochberg / Abstract: The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an ...The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14178.map.gz | 230.3 MB | EMDB map data format | |
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Header (meta data) | emd-14178-v30.xml emd-14178.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_14178.png | 53.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14178 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14178 | HTTPS FTP |
-Validation report
Summary document | emd_14178_validation.pdf.gz | 512.2 KB | Display | EMDB validaton report |
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Full document | emd_14178_full_validation.pdf.gz | 511.7 KB | Display | |
Data in XML | emd_14178_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_14178_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14178 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14178 | HTTPS FTP |
-Related structure data
Related structure data | 7qviMC 7qsvC 7qswC 7qsxC 7qsyC 7qszC 7qt1C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14178.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : ancestral sequence reconstruction of RubisCO large subunit in com...
Entire | Name: ancestral sequence reconstruction of RubisCO large subunit in complex with CABP and Magnesium |
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Components |
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-Supramolecule #1: ancestral sequence reconstruction of RubisCO large subunit in com...
Supramolecule | Name: ancestral sequence reconstruction of RubisCO large subunit in complex with CABP and Magnesium type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: complex of two octamers (2x L8) |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Recombinant strain: ArtricExpress (DE3) |
Molecular weight | Experimental: 873 KDa |
-Macromolecule #1: RubisCO large subunit
Macromolecule | Name: RubisCO large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.19693 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MARAQYEAGV RPYRETYYDP DYEPKDTDLL CAFRITPKPG VPMEEAAAAV AAESSTGTWT EVWSNLLTDL ERYKARCYRI EGDVAYIAY PLDLFEEGSI VNIMSSIVGN VFGFKAVQAL RLEDMRIPVA YLKTFPGPPT GIQVERDRLN KYGRPLLGGT I KPKLGLSA ...String: MARAQYEAGV RPYRETYYDP DYEPKDTDLL CAFRITPKPG VPMEEAAAAV AAESSTGTWT EVWSNLLTDL ERYKARCYRI EGDVAYIAY PLDLFEEGSI VNIMSSIVGN VFGFKAVQAL RLEDMRIPVA YLKTFPGPPT GIQVERDRLN KYGRPLLGGT I KPKLGLSA KEYARVVYEC LRGGLDTT(KCX)D DENLNSQPFN RWRDRFLYVM EAVRKAEAET GERKGHWLNV TAGSTEEM L KRAEFAAELG SRYIMVDFLT AGFAAFASVR RRAEELGLML HCHRAMHAVF DRQPNHGIHF RVLAKWLRMV GGDHVHTGT VVGKLEGDRA ETLGIADLLR EDYVPADPGR GLFFDQDWAG LKPVFPVASG GIHVWHVPDL VSIFGDDAFF LFGGGTHGHP RGSRAGATA NRVAVEAVVQ ARNEGRDILA EGREILEEAA RWCPELREAM ELWGDVKFEV EA |
-Macromolecule #2: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Macromolecule | Name: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: CAP |
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Molecular weight | Theoretical: 356.115 Da |
Chemical component information | ChemComp-CAP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 2D array |
-Sample preparation
Concentration | 1 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171572 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |