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- EMDB-33524: Cryo-EM strutcure of a assembly intermediate RbcL8Raf18RbcX16 -

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Basic information

Entry
Database: EMDB / ID: EMD-33524
TitleCryo-EM strutcure of a assembly intermediate RbcL8Raf18RbcX16
Map data
Sample
  • Complex: The termary complex of RbcL-Raf1-RbcX
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily ...Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / RuBisCO chaperone RbcX / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / 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
RuBisCO chaperone RbcX / Ribulose bisphosphate carboxylase large chain / RuBisCO accumulation factor 1
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJiang YL / Xia LY
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 and XDB37020301 China
National Natural Science Foundation of China (NSFC)32171198 China
Ministry of Science and Technology (MoST, China)2016YFA0400900 China
CitationJournal: Cell Discov / Year: 2022
Title: Structural insights into cyanobacterial RuBisCO assembly coordinated by two chaperones Raf1 and RbcX.
Authors: Qiong Li / Yong-Liang Jiang / Ling-Yun Xia / Yuxing Chen / Cong-Zhao Zhou /
Abstract: RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series ...RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series of chaperones that include RbcX and RuBisCO accumulation factor 1 (Raf1). To understand how these RuBisCO-specific chaperones function during cyanobacterial RbcLRbcS (LS) holoenzyme formation, we solved a 3.3-Å cryo-electron microscopy structure of a 32-subunit RbcLRaf1RbcX (LFX) assembly intermediate from Anabaena sp. PCC 7120. Comparison to the previously resolved LF and LX structures together with biochemical assays revealed that the LFX complex forms a rather dynamic structural intermediate, favoring RbcS displacement of Raf1 and RbcX. In vitro assays further demonstrated that both Raf1 and RbcX function to regulate RuBisCO condensate formation by restricting CcmM35 binding to the stably assembled LS holoenzymes. Combined with previous findings, we propose a model on how Raf1 and RbcX work in concert to facilitate, and regulate, cyanobacterial RuBisCO assembly as well as disassembly of RuBisCO condensates.
History
DepositionJun 2, 2022-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33524.png

Downloads & links

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Map

FileDownload / File: emd_33524.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 280 pix.
= 282.8 Å		1.01 Å/pix.
x 280 pix.
= 282.8 Å		1.01 Å/pix.
x 280 pix.
= 282.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.04984373 - 0.09631843
Average (Standard dev.)0.00024845594 (±0.0043827593)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 282.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33524_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_33524_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The termary complex of RbcL-Raf1-RbcX

EntireName: The termary complex of RbcL-Raf1-RbcX
Components
  • Complex: The termary complex of RbcL-Raf1-RbcX

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Supramolecule #1: The termary complex of RbcL-Raf1-RbcX

SupramoleculeName: The termary complex of RbcL-Raf1-RbcX / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 1.05 MDa

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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: 8 / Details: 50 mM Tris-HCl, pH 8.0, 20 mM NaCl, 5 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kkm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54260
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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