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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0959 | ||||||||||||||||||
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Title | Cryo-EM structure of RuBisCO-Raf1 from Anabaena sp. PCC 7120 | ||||||||||||||||||
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Function / homology | ![]() ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||||||||||||||
![]() | Xia LY / Jiang YL / Kong WW / Chen Y / Zhou CZ | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1. Authors: Ling-Yun Xia / Yong-Liang Jiang / Wen-Wen Kong / Hui Sun / Wei-Fang Li / Yuxing Chen / Cong-Zhao Zhou / ![]() Abstract: The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and ...The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and plants. Here, we report the crystal structures of Raf1 from cyanobacteria Anabaena sp. PCC 7120 and its complex with RuBisCO large subunit RbcL. Structural analyses and biochemical assays reveal that each Raf1 dimer captures an RbcL dimer, with the C-terminal tail inserting into the catalytic pocket, and further mediates the assembly of RbcL dimers to form the octameric core of RuBisCO. Furthermore, the cryo-electron microscopy structures of the RbcL-Raf1-RbcS assembly intermediates enable us to see a dynamic assembly process from RbcLRaf1 to the holoenzyme RbcLRbcS. In vitro assays also indicate that Raf1 can attenuate and reverse CcmM-mediated cyanobacterial RuBisCO condensation. Combined with previous findings, we propose a putative model for the assembly of cyanobacterial RuBisCO coordinated by the chaperone Raf1. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
Images | ![]() | 61.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 505 KB | Display | ![]() |
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Full document | ![]() | 504.6 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 6.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lrrMC ![]() 0960C ![]() 0961C ![]() 0962C ![]() 6kkmC ![]() 6kknC ![]() 6lrsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Ternary complex of RuBisCO with the chaperone Raf1
Entire | Name: Ternary complex of RuBisCO with the chaperone Raf1 |
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Components |
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-Supramolecule #1: Ternary complex of RuBisCO with the chaperone Raf1
Supramolecule | Name: Ternary complex of RuBisCO with the chaperone Raf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 900 KDa |
-Macromolecule #1: All5250 protein
Macromolecule | Name: All5250 protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 18.391881 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QRPAPIPPFF RFDTEDELPR IVPVVGQLPL KAEELKAVPL VEEIEPFRLV KFSGEQAWVA LPGWQVLLAA EDPVTILATS DRFPKQNQT EPGPVLVVVD RSQREWNDFS YFVVDHDGEL DFQWFETKPE FPILGKVIIL VRPRRILDEN VTKDSWQIDE |
-Macromolecule #2: Ribulose bisphosphate carboxylase small chain
Macromolecule | Name: Ribulose bisphosphate carboxylase small chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 12.840725 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREVL AEVQSCRSQY PGHYIRVVG FDNIKQCQIL SFIVHKPSRY |
-Macromolecule #3: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 53.112125 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR ...String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTTV WTDLLTDLDR YKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT SIVGNVFGFK ALRALRLEDI RFPVAYIKTF QGPPHGIQVE R DKLNKYGR PLLGCTIKPK LGLSAKNYGR AVYECLRGGL DFTKDDENIN SAPFQRWRDR FLFVADAITK AQAETGEIKG HY LNVTAPT CEEMLKRAEY AKELKQPIIM HDYLTAGFTA NTTLARWCRD NGVLLHIHRA MHAVIDRQKN HGIHFRVLAK ALR LSGGDH IHTGTVVGKL EGERGITMGF VDLLRENYVE QDKSRGIYFT QDWASLPGVM AVASGGIHVW HMPALVEIFG DDSV LQFGG GTLGHPWGNA PGATANRVAL EACVQARNEG RNLAREGNDV IREAAKWSPE LAVACELWKE IKFEFEAMDT V |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 149382 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: ANGULAR RECONSTITUTION |