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- EMDB-70520: A. agrestis Rubisco (8 RbcL 7 RbcS 1 RbcS-STAR) -

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Basic information

Entry
Database: EMDB / ID: EMD-70520
TitleA. agrestis Rubisco (8 RbcL 7 RbcS 1 RbcS-STAR)
Map dataA. agrestis Rubisco (8 RbcL 7 RbcS1 1 RbcS-STAR)
Sample
  • Complex: A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR)
    • Other: Rubisco Large Subunit
    • Other: Rubisco Small Subunit
    • Other: Rubisco Small Subunit - SequesTration Associated Region (RbcS-STAR)
KeywordsAnthoceros agrestis rubisco / pyrenoid / synbio / rubisco linker / PHOTOSYNTHESIS
Biological speciesAnthoceros agrestis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 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: Science / Year: 2026
Title: An unconventional Rubisco small subunit underpins the CO-concentrating organelle in land plants.
Authors: Tanner A Robison / Yuwei Mao / Zhen Guo Oh / Warren S L Ang / Dan Hong Loh / Yu-Heng Hsieh / Maddie Ceminsky / Nicky Atkinson / Declan Lafferty / Xia Xu / Laura H Gunn / Alistair J McCormick / Fay-Wei Li /
Abstract: In many algae, photosynthesis is boosted by biophysical CO-concentrating mechanisms, which pack the CO-fixing enzyme Rubisco into liquid-like organelles called pyrenoids. Engineering C crops with ...In many algae, photosynthesis is boosted by biophysical CO-concentrating mechanisms, which pack the CO-fixing enzyme Rubisco into liquid-like organelles called pyrenoids. Engineering C crops with algal pyrenoids could increase yields, but progress is hampered by the deep evolutionary divide between crops and algae. Here, we show that hornworts, the only land plants with pyrenoids, have an unusual Rubisco small subunit, RbcS-STAR, the C-terminal coiled-coil domain of which oligomerizes to mediate Rubisco condensation. RbcS-STAR is incorporated into the Rubisco holoenzyme and thus acts as an "innate" Rubisco linker. Expression of RbcS-STAR in pyrenoid-lacking species, including , is sufficient to induce pyrenoid-like condensates. Our findings reveal a mechanism for Rubisco condensation and a potential route to introduce pyrenoids into crop plants.
History
DepositionMay 6, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70520.png

Downloads & links

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Map

FileDownload / File: emd_70520.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA. agrestis Rubisco (8 RbcL 7 RbcS1 1 RbcS-STAR)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375
Minimum - Maximum-0.09771554 - 0.75752115
Average (Standard dev.)0.0051334156 (±0.022484567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR)

EntireName: A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR)
Components
  • Complex: A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR)
    • Other: Rubisco Large Subunit
    • Other: Rubisco Small Subunit
    • Other: Rubisco Small Subunit - SequesTration Associated Region (RbcS-STAR)

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Supramolecule #1: A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR)

SupramoleculeName: A. agrestis Rubisco (8 RbcL, 7 RbcS, 1 RbcS-STAR) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anthoceros agrestis (plant)
Molecular weightTheoretical: 0.55 kDa/nm

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Macromolecule #1: Rubisco Large Subunit

MacromoleculeName: Rubisco Large Subunit / type: other / ID: 1 / Classification: other
Source (natural)Organism: Anthoceros agrestis (plant)
SequenceString: MSPQTETKAG VGFKAGVKDY RLTYYTPDYE TKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV AGEENQYIAY VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYSKTFQG PPHGIQVERD KLNKYGRPLL ...String:
MSPQTETKAG VGFKAGVKDY RLTYYTPDYE TKDTDILAAF RMTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYDIEPV AGEENQYIAY VAYPLDLFEE GSVTNMFTSI VGNVFGFKAL RALRLEDLRI PPAYSKTFQG PPHGIQVERD KLNKYGRPLL GCTIKPKLGL SAKNYGRAVY ECLRGGLDFT KDDENVNSQP FMRWRDRFLF VAEAIFKSQA ETGEIKGHYL NATAGTCEEM MKRAQFAREL GMPIVMHDYL TGGFTANTTL AHYCRDNGLL LHIHRAMHAV IDRQRNHGIH FRVLAKALRM SGGDHIHSGT VVGKLEGERE VTLGFVDLLR DDYIEKDRSR GIYFTQDWVS MPGVLPVASG GIHVWHMPAL TEIFGDDSVL QFGGGTLGHP WGNAPGAVAN RVALEACVQA RNEGRDLARE GNDIIREASK WSPELAAACE VWKEIKFVFE TIDTL
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #2: Rubisco Small Subunit

MacromoleculeName: Rubisco Small Subunit / type: other / ID: 2 / Classification: other
Source (natural)Organism: Anthoceros agrestis (plant)
SequenceString:
MQVWNPIDNP KFETLSYLPP LTDNQIAREI DYMLRNKWIP CLEFDPSGTI TTLPGQPGYY GGRYWTMWKL PMFGCNNAGY VLREIEHCKN AYPGCFIRVL GFDNIRQVQC CAFIVHKPQH HHHHH
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #3: Rubisco Small Subunit - SequesTration Associated Region (RbcS-STAR)

MacromoleculeName: Rubisco Small Subunit - SequesTration Associated Region (RbcS-STAR)
type: other / ID: 3 / Classification: other
Source (natural)Organism: Anthoceros agrestis (plant)
SequenceString: MQVWTPVDNK KFETLSYLPA LSSNQIAKQI DFMLSKGWIP CLEFDKSAEL KVVRGQPGFY NGRYWTMWKL PMFGCNDASS VLREVENCRK AYPNCYIRVL GFDNQRQVQC SAFIVHKPVK NALTEKLDRS LAKPAYKPQP QVSSVVTSRS GWSRDVEVYQ PKDDKTVVDK ...String:
MQVWTPVDNK KFETLSYLPA LSSNQIAKQI DFMLSKGWIP CLEFDKSAEL KVVRGQPGFY NGRYWTMWKL PMFGCNDASS VLREVENCRK AYPNCYIRVL GFDNQRQVQC SAFIVHKPVK NALTEKLDRS LAKPAYKPQP QVSSVVTSRS GWSRDVEVYQ PKDDKTVVDK INSLQAGLDG LQRELALLRA SAAHDKIKIL QGALDGLQRE ISVLRASVGH TV
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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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

Concentration1 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 / Mesh: 400 / Support film - Material: CARBON / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 for 4 seconds.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4222 / Average electron dose: 50.0 e/Å2 / Details: Images were collected over 40 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: 825654
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Software - details: Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9chz

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 35660
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final 3D classificationNumber classes: 8 / Avg.num./class: 10000 / Software - Name: cryoSPARC (ver. 4)

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