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- EMDB-70090: Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70090
TitleCryo-EM structure of Rubisco with hetero small subunit 1A3B form I
Map data
Sample
  • Complex: rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
Keywordsrubisco / Arabidopsis thaliana / hetero small subunit / PLANT PROTEIN
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 / protein domain specific 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 / Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhang Z / Bolla J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I
Authors: Zhang Z / Bolla J
History
DepositionApr 8, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70090.png

Downloads & links

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Map

FileDownload / File: emd_70090.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.55803883 - 1.108062
Average (Standard dev.)0.0006139481 (±0.04556003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70090_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_70090_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 3B, chloroplastic
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic

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Supramolecule #1: rubisco

SupramoleculeName: rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 53.020883 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 DSVL 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 3B, chloroplastic

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 20.307338 KDa
SequenceString:
MASSMLSSAA VVTSPAQATM VAPFTGLKSS AAFPVTRKTN KDITSIASNG GRVSCMKVWP PIGKKKFETL SYLPDLSDVE LAKEVDYLL RNKWIPCVEF ELEHGFVYRE HGNTPGYYDG RYWTMWKLPL FGCTDSAQVL KEVEECKKEY PGAFIRIIGF D NTRQVQCI SFIAYKPPSF TEA

UniProtKB: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic

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Macromolecule #3: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14328
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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