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- EMDB-62834: CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-62834
TitleCryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Map data
Sample
  • Complex: Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
  • Ligand: SULFATE ION
  • Ligand: water
KeywordsCO2 fixation / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid lumen / salicylic acid binding / ribulose bisphosphate carboxylase complex assembly / chloroplast membrane / plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid ...thylakoid lumen / salicylic acid binding / ribulose bisphosphate carboxylase complex assembly / chloroplast membrane / 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 / photosynthesis / cytosolic ribosome / response to cold / chloroplast / monooxygenase activity / copper ion binding / mRNA binding / magnesium ion binding / mitochondrion
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. ...Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / 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 / Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.74 Å
AuthorsYamori W / Nakazato I / Yuchen Q / Sanga Y / Miyata T / Uehara R / Noto Y / Namba K / Fukayama H / Matsumura H / Arimura S
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24H02277 Japan
Japan Society for the Promotion of Science (JSPS)24K01994 Japan
Japan Society for the Promotion of Science (JSPS)23K18033 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Science and TechnologyJPMJOP1861 Japan
CitationJournal: To Be Published
Title: CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Authors: Yamori W / Nakazato I / Yuchen Q / Sanga Y / Miyata T / Uehara R / Noto Y / Namba K / Fukayama H / Matsumura H / Arimura S
History
DepositionDec 23, 2024-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62834.png

Downloads & links

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Map

FileDownload / File: emd_62834.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å		0.87 Å/pix.
x 256 pix.
= 222.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.27705887 - 0.5879331
Average (Standard dev.)-0.00011410263 (±0.016574884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 222.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62834_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_62834_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

EntireName: Rubisco
Components
  • Complex: Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
  • Ligand: SULFATE ION
  • Ligand: water

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Supramolecule #1: Rubisco

SupramoleculeName: Rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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)
Molecular weightTheoretical: 53.019898 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 FTKDDENVNS QPFMRWRDRF LFCAEAIYKS QAETGEIKGH YL NATAGTC EEMIKRAVFA RELGVPIVMH DYLTGGFTAN TSLSHYCRDN GLLLHIHRAM HAVIDRQKNH GMHFRVLAKA LRL SGGDHI HAGTVVGKLE GDRESTLGFV DLLRDDYVEK DRSRGIFFTQ DWVSLPGVLP VASGGIHVWH MPALTEIFGD NSVL QFGGG TLGHPWGNAP GAVANRVALE ACVQARNEGR DLAVEGNEII REACKWSPEL AAACEVWKEI TFNFPTIDKL DGQE

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #2: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
type: protein_or_peptide / ID: 2
Details: The amino acid sequences of RBCS2B and RBCS3B, which cause microheterogeneity, are registered in GenBank under accession numbers AAO29974.1 and AAL47390.1.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.237104 KDa
SequenceString:
MASSMLSSAT MVASPAQATM VAPFNGLKSS AAFPATRKAN NDITSITSNG GRVNCMQVWP PIGKKKFETL SYLPDLTDSE LAKEVDYLI RNKWIPCVEF ELEHGFVYRE HGNSPGYYDG RYWTMWKLPL FGCTDSAQVL KEVEECKKEY PNAFIRIIGF D NTRQVQCI SFIAYKPPSF TG

UniProtKB: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic

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Macromolecule #3: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2324 / 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 / Component - Concentration: 50.0 mM / Component - Formula: (NH4)2SO4 / Component - Name: ammonium sulfate
Details: 80 mM HEPES-KOH pH 8.0, 5 mM DTT, 1 mM EDTA, 50 mM ammonium sulfate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2732 / Average exposure time: 3.2 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2302408
CTF correctionSoftware - Name: CTFFIND / 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: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 904485
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6kyi

chain_id: A, residue_range: 21-464, source_name: PDB, initial_model_type: experimental model

6kyi

chain_id: B, residue_range: 20-462, source_name: PDB, initial_model_type: experimental model

6kyi

chain_id: S, residue_range: 1-119, source_name: PDB, initial_model_type: experimental model

6kyi

chain_id: T, residue_range: 1-120, source_name: PDB, initial_model_type: experimental model
Output model

PDB-9l5i:
CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry

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