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- EMDB-71937: Hybrid Rubisco containing Arabidopsis thaliana large subunit and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-71937
TitleHybrid Rubisco containing Arabidopsis thaliana large subunit and Limonium gibertii small subunit
Map data
Sample
  • Complex: Rubisco containing Arabidopsis thaliana large subunit and Nicotiana tabacum trichome isoform 2 small subunit
    • Complex: Arabidopsis thaliana Rubisco large subunit
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Complex: Limonium gibertii Rubisco small subunit
      • Protein or peptide: Rubisco small subunit
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordscarboxylase / oxygenase / TIM barrel / Calvin-Benson-Bassham Cycle / PHOTOSYNTHESIS
Function / homology
Function and homology information


plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid / reductive pentose-phosphate cycle / response to abscisic acid / chloroplast envelope / chloroplast stroma ...plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid / reductive pentose-phosphate cycle / response to abscisic acid / chloroplast envelope / chloroplast stroma / plastid / chloroplast thylakoid membrane / response to cadmium ion / monooxygenase activity / chloroplast / cytosolic ribosome / mRNA binding / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco) / Arabidopsis thaliana (thale cress) / Limonium gibertii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.12 Å
AuthorsAzinas S / Ceminsky M / Gunn LH
Funding support Sweden, United States, 2 items
OrganizationGrant numberCountry
Carl Trygger Foundation Sweden
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Heterologous small subunits complement growth and modify Rubisco catalysis in Arabidopsis
Authors: Mao Y / Azinas S / Ceminsky M / Orr D / Gunn LH / McCormick AJ
History
DepositionAug 5, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71937.png

Downloads & links

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Map

FileDownload / File: emd_71937.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 384 pix.
= 254.976 Å		0.66 Å/pix.
x 384 pix.
= 254.976 Å		0.66 Å/pix.
x 384 pix.
= 254.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.211
Minimum - Maximum-0.84895396 - 1.63036
Average (Standard dev.)0.0015954506 (±0.06410785)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 254.97598 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71937_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71937_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 : Rubisco containing Arabidopsis thaliana large subunit and Nicotia...

EntireName: Rubisco containing Arabidopsis thaliana large subunit and Nicotiana tabacum trichome isoform 2 small subunit
Components
  • Complex: Rubisco containing Arabidopsis thaliana large subunit and Nicotiana tabacum trichome isoform 2 small subunit
    • Complex: Arabidopsis thaliana Rubisco large subunit
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Complex: Limonium gibertii Rubisco small subunit
      • Protein or peptide: Rubisco small subunit
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Rubisco containing Arabidopsis thaliana large subunit and Nicotia...

SupramoleculeName: Rubisco containing Arabidopsis thaliana large subunit and Nicotiana tabacum trichome isoform 2 small subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Nicotiana tabacum (common tobacco)
Molecular weightTheoretical: 14 KDa

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Supramolecule #2: Arabidopsis thaliana Rubisco large subunit

SupramoleculeName: Arabidopsis thaliana Rubisco large subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: 1a2b3b
Molecular weightTheoretical: 550 KDa

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Supramolecule #3: Limonium gibertii Rubisco small subunit

SupramoleculeName: Limonium gibertii Rubisco small subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: RbcS2
Source (natural)Organism: Limonium gibertii (plant)

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Macromolecule #1: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: 1a2b3b
Molecular weightTheoretical: 53.063883 KDa
SequenceString: MSPQTETKAS VGFKAGVKEY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEP VPGEETQFIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LAALRLEDLR IPPAYTKTFQ GPPHGIQVER D KLNKYGRP ...String:
MSPQTETKAS VGFKAGVKEY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEP VPGEETQFIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LAALRLEDLR IPPAYTKTFQ GPPHGIQVER D KLNKYGRP LLGCTIKPKL GLSAKNYGRA VYECLRGGLD FT(KCX)DDENVNS QPFMRWRDRF LFCAEAIYKS QAETGEIK G HYLNATAGTC EEMIKRAVFA RELGVPIVMH DYLTGGFTAN TSLSHYCRDN GLLLHIHRAM HAVIDRQKNH GMHFRVLAK ALRLSGGDHI HAGTVVGKLE GDRESTLGFV DLLRDDYVEK DRSRGIFFTQ DWVSLPGVLP VASGGIHVWH MPALTEIFGD DSVLQFGGG TLGHPWGNAP GAVANRVALE ACVQARNEGR DLAVEGNEII REACKWSPEL AAACEVWKEI TFNFPTIDKL D GQE

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #2: Rubisco small subunit

MacromoleculeName: Rubisco small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: 1a2b3b
Molecular weightTheoretical: 14.40764 KDa
SequenceString:
MQVWPPEGLK KFETLSYLPP LDREGLANEI SYLMRMGWVP CLEFEVGEAY IHREYHNLPG YYDGRYWTMW KLPMFGCTDP AQVLKEVDE CSKLYPHAHI RILGFDNKRQ VQCISFIAYK PPS

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Macromolecule #3: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 1482 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8305 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2974987
CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 645919
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5iu0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9pwp:
Hybrid Rubisco containing Arabidopsis thaliana large subunit and Limonium gibertii small subunit

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