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- EMDB-45608: Anthoceros agrestis Rubisco octamer core complexed with small sub... -

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Basic information

Entry
Database: EMDB / ID: EMD-45608
TitleAnthoceros agrestis Rubisco octamer core complexed with small subunits and Arabidopsis thaliana BSD2
Map dataAnthoceros agrestis Rubisco assembled intermediate complex. Octamer core bound to 4 units of small subunit and 4 units of BSD2.
Sample
  • Complex: Rubisco assembly intermediate
    • Protein or peptide: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
    • Protein or peptide: Rubisco large subunit
    • Protein or peptide: Rubisco small subunit
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
KeywordsAnthoceros agrestis rubisco / PHOTOSYNTHESIS
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / chloroplast / metal ion binding / cytosol
Similarity search - Function
Heat shock protein DnaJ, cysteine-rich domain superfamily
Similarity search - Domain/homology
Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
Similarity search - Component
Biological speciesAnthoceros agrestis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsAng WSL / Oh ZG / Li FW / Gunn LH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB2213840 United States
National Science Foundation (NSF, United States)MCB2213841 United States
CitationJournal: Mol Plant / Year: 2024
Title: Unique biogenesis and kinetics of hornwort Rubiscos revealed by synthetic biology systems.
Authors: Zhen-Guo Oh / Tanner Ashton Robison / Dan-Hong Loh / Warren Shou Leong Ang / Jediael Ng / Fay-Wei Li / Laura Helen Gunn /
Abstract: Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco's CO fixation. Yet, hornwort Rubisco remains poorly characterized. Here we assemble the hornwort Anthoceros agrestis ...Hornworts are the only land plants that employ a pyrenoid to optimize Rubisco's CO fixation. Yet, hornwort Rubisco remains poorly characterized. Here we assemble the hornwort Anthoceros agrestis Rubisco (AaRubisco) using the Arabidopsis thaliana SynBio expression system and observed the formation of stalled intermediates, prompting us to develop a new SynBio system with A. agrestis cognate chaperones. We successfully assembled AaRubisco and Rubisco from three other hornwort species. Unlike A. thaliana Rubisco, AaRubisco assembly is not dependent on RbcX or Raf2. Kinetic characterization reveals that hornwort Rubiscos exhibit a range of catalytic rates (3-10 s), but with similar affinity (∼30 μM) and specificity (∼70) for CO. In other words, hornwort Rubiscos do not comply with the long held canonical catalytic trade-off observed in other land plants, providing experimental support that Rubisco kinetics may be phylogenetically constrained. Unexpectedly, we observed a 50% increase in AaRubisco catalytic rates when RbcX was removed from our SynBio system, without any reduction in specificity. Structural biology, biochemistry and proteomic analysis suggest that subtle differences in Rubisco large subunit interactions, when RbcX is absent during biogenesis, increases the accessibility of active sites and catalytic turnover rate. This study uncovered a previously unknown Rubisco kinetic parameter space and provides a SynBio chassis to expand the survey of other Rubisco kinetics. Our discovery could thus reshape the approaches for engineering Rubisco with superior kinetics.
History
DepositionJul 2, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45608.png

Downloads & links

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Map

FileDownload / File: emd_45608.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnthoceros agrestis Rubisco assembled intermediate complex. Octamer core bound to 4 units of small subunit and 4 units of BSD2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.55 Å/pix.
x 512 pix.
= 281.6 Å		0.55 Å/pix.
x 512 pix.
= 281.6 Å		0.55 Å/pix.
x 512 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.55 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.23049761 - 0.4460757
Average (Standard dev.)0.0007609335 (±0.021431286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_45608_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45608_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rubisco assembly intermediate

EntireName: Rubisco assembly intermediate
Components
  • Complex: Rubisco assembly intermediate
    • Protein or peptide: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
    • Protein or peptide: Rubisco large subunit
    • Protein or peptide: Rubisco small subunit
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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Supramolecule #1: Rubisco assembly intermediate

SupramoleculeName: Rubisco assembly intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Anthoceros agrestis (plant)
Molecular weightTheoretical: 510 KDa

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Macromolecule #1: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic

MacromoleculeName: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 14.560366 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MANSLCFFSS PPTFCFQSPS KNPKPSHFFS TNDNTSSLVQ KRELLQTSRS QSFEVKAANN NPQGTKPNSL VCANCEGEGC VACSQCKGG GVNLIDHFNG QFKAGALCWL CRGKKEVLCG DCNGAGFIGG FLSTFDE

UniProtKB: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic

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Macromolecule #2: Rubisco large subunit

MacromoleculeName: Rubisco large subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Anthoceros agrestis (plant)
Molecular weightTheoretical: 52.908777 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSPQTETKAG VGFKAGVKDY RLTYYTPDYE TKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VAGEENQYIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LRALRLEDLR IPPAYSKTFQ GPPHGIQVER D KLNKYGRP ...String:
MSPQTETKAG VGFKAGVKDY RLTYYTPDYE TKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEP VAGEENQYIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LRALRLEDLR IPPAYSKTFQ GPPHGIQVER D KLNKYGRP LLGCTIKPKL GLSAKNYGRA VYECLRGGLD FT(KCX)DDENVNS QPFMRWRDRF LFVAEAIFKS QAETGEIK G HYLNATAGTC EEMMKRAQFA RELGMPIVMH DYLTGGFTAN TTLAHYCRDN GLLLHIHRAM HAVIDRQRNH GIHFRVLAK ALRMSGGDHI HSGTVVGKLE GEREVTLGFV DLLRDDYIEK DRSRGIYFTQ DWVSMPGVLP VASGGIHVWH MPALTEIFGD DSVLQFGGG TLGHPWGNAP GAVANRVALE ACVQARNEGR DLAREGNDII REASKWSPEL AAACEVWKEI KFVFETIDTL

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Macromolecule #3: Rubisco small subunit

MacromoleculeName: Rubisco small subunit / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Anthoceros agrestis (plant)
Molecular weightTheoretical: 14.70791 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQVWNPIDNP KFETLSYLPP LTDNQIAREI DYMLRNKWIP CLEFDPSGTI TTLPGQPGYY GGRYWTMWKL PMFGCNNAGY VLREIEHCK NAYPGCFIRV LGFDNIRQVQ CCAFIVHKPQ HHHHHH

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
50.0 mMNaClSodium chloride

Details: 20 mM Tris pH 8.0 50 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 4.8 sec. / Average electron dose: 65.0 e/Å2 / Details: Images were collected over 50 movie frames
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 79000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 522687
Startup modelType of model: OTHER
Details: Starting model from pdb 9CHZ from our associated deposition. BSD2 from 8ILM and 8ILB, and rigid body docked.
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Software - details: Homogeneous refinement / Number images used: 19751
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 183580 / Software - Name: cryoSPARC (ver. 4) / Software - details: 3D classification tool

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Atomic model buiding 1

Initial model
PDB IDChain

9chz

chain_id: all, source_name: PDB, initial_model_type: experimental model

8lim

source_name: PDB, initial_model_type: experimental model

8ilb

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9ci2:
Anthoceros agrestis Rubisco octamer core complexed with small subunits and Arabidopsis thaliana BSD2

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