+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0960 | ||||||||||||||||||
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Title | Cryo-EM structure of RbcL8-RbcS4 from Anabaena sp. PCC 7120 | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Nostoc sp. PCC 7120 (bacteria) / Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||||||||||||||
Authors | Xia LY / Jiang YL / Kong WW / Sun H / Li WF / Chen Y / Zhou CZ | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: Nat Plants / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0960.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-0960-v30.xml emd-0960.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_0960.png | 62.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0960 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0960 | HTTPS FTP |
-Validation report
Summary document | emd_0960_validation.pdf.gz | 532.7 KB | Display | EMDB validaton report |
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Full document | emd_0960_full_validation.pdf.gz | 532.2 KB | Display | |
Data in XML | emd_0960_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_0960_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0960 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0960 | HTTPS FTP |
-Related structure data
Related structure data | 6lrsMC 0959C 0961C 0962C 6kkmC 6kknC 6lrrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0960.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
-Entire : The complex of RbcL8-RbcS4
Entire | Name: The complex of RbcL8-RbcS4 |
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Components |
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-Supramolecule #1: The complex of RbcL8-RbcS4
Supramolecule | Name: The complex of RbcL8-RbcS4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Nostoc sp. PCC 7120 (bacteria) |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Molecular weight | Theoretical: 900 KDa |
-Macromolecule #1: Ribulose bisphosphate carboxylase small chain
Macromolecule | Name: Ribulose bisphosphate carboxylase small chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 12.840725 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREVL AEVQSCRSQY PGHYIRVVG FDNIKQCQIL SFIVHKPSRY |
-Macromolecule #2: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large 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: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 |
Molecular weight | Theoretical: 53.112125 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |