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- EMDB-14178: Fiber-forming RubisCO derived from ancestral sequence reconstruct... -

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Basic information

Entry
Database: EMDB / ID: EMD-14178
TitleFiber-forming RubisCO derived from ancestral sequence reconstruction and rational engineering
Map data
Sample
  • Complex: ancestral sequence reconstruction of RubisCO large subunit in complex with CABP and Magnesium
    • Protein or peptide: RubisCO large subunitRuBisCO
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSchulz L / Zarzycki J / Prinz S / Schuller JM / Erb TJ / Hochberg GKA
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SCHU 3364/1-1 Germany
CitationJournal: 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
DepositionJan 21, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14178.png

Downloads & links

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Map

FileDownload / File: emd_14178.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 334.8 Å		0.84 Å/pix.
x 400 pix.
= 334.8 Å		0.84 Å/pix.
x 400 pix.
= 334.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.51782227 - 0.86381006
Average (Standard dev.)0.0005547703 (±0.039316826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 334.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ancestral sequence reconstruction of RubisCO large subunit in com...

EntireName: ancestral sequence reconstruction of RubisCO large subunit in complex with CABP and Magnesium
Components
  • Complex: ancestral sequence reconstruction of RubisCO large subunit in complex with CABP and Magnesium
    • Protein or peptide: RubisCO large subunitRuBisCO
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ancestral sequence reconstruction of RubisCO large subunit in com...

SupramoleculeName: 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)
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Recombinant strain: ArtricExpress (DE3)
Molecular weightExperimental: 873 KDa

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Macromolecule #1: RubisCO large subunit

MacromoleculeName: RubisCO large subunit / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.19693 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: 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

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Macromolecule #2: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

ChemComp-CAP:
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC6H13NO5Tricine
75.0 mMNaClSodium chloridesodium chloride
0.07 mMC6H14O13P2CABPFrozen state pension
1.33 mMMgCl2magnesium chloride
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7qsx

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171572

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