+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0961 | ||||||||||||||||||
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Title | The RuBisCO assembly intermediate RbcL-RbcS-Raf1 (L8S4F8) | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Biological species | Nostoc sp. PCC 7120 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 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_0961.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-0961-v30.xml emd-0961.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_0961.png | 70.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0961 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0961 | HTTPS FTP |
-Validation report
Summary document | emd_0961_validation.pdf.gz | 79.4 KB | Display | EMDB validaton report |
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Full document | emd_0961_full_validation.pdf.gz | 78.5 KB | Display | |
Data in XML | emd_0961_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0961 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0961 | HTTPS FTP |
-Related structure data
Related structure data | 0959C 0960C 0962C 6kkmC 6kknC 6lrrC 6lrsC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0961.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 : Ternary complex of RuBisCO with chaperone Raf1
Entire | Name: Ternary complex of RuBisCO with chaperone Raf1 |
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Components |
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-Supramolecule #1: Ternary complex of RuBisCO with chaperone Raf1
Supramolecule | Name: Ternary complex of RuBisCO with chaperone Raf1 / 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: 850 KDa |
-Macromolecule #1: RuBisCO accumulation factor Raf1
Macromolecule | Name: RuBisCO accumulation factor Raf1 / type: other / ID: 1 / Classification: other |
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Sequence | String: QRPAPIPPFF RFDTEDELPR IVPVVGQLPL KAEELKAV P LVEEIEPFRL VKFSGEQAWV ALPGWQVLLA AEDPVTILAT SDRFPKQNQT EPGPVLVVV DRSQREWNDF SYFVVDHDGE LDFQWFETKP EFPILGKVII LVRPRRILDE NVTKDSWQID E |
-Macromolecule #2: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN
Macromolecule | Name: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN / type: other / ID: 2 / Classification: other |
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Sequence | String: MQTLPKERRY ETLSYLPPLT DVQIEKQVQY ILSQGYIPAV EFNEVSEPTE LYWTLWKLPL FGAKTSREV LAEVQSCRSQ YPGHYIRVVG FDNIKQCQIL SFIVHKPSRY |
-Macromolecule #3: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN
Macromolecule | Name: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN / type: other / ID: 3 / Classification: other |
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Sequence | String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTT VWTDLLTDLD RYKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT S IVGNVFGF KALRALRLED IRFPVAYIKT FQGPPHGIQV ERDKLNKYGR ...String: MSYAQTKTQT KSGYKAGVQD YRLTYYTPDY TPKDTDILAA FRVTPQPGVP FEEAAAAVAA ESSTGTWTT VWTDLLTDLD RYKGRCYDIE PVPGEDNQFI AYIAYPLDLF EEGSITNVLT S IVGNVFGF KALRALRLED IRFPVAYIKT FQGPPHGIQV ERDKLNKYGR PLLGCTIKPK LG LSAKNYG RAVYECLRGG LDFTKDDENI NSAPFQRWRD RFLFVADAIT KAQAETGEIK GHY LNVTAP TCEEMLKRAE YAKELKQPII MHDYLTAGFT ANTTLARWCR DNGVLLHIHR AMHA VIDRQ KNHGIHFRVL AKALRLSGGD HIHTGTVVGK LEGERGITMG FVDLLRENYV EQDKS RGIY FTQDWASLPG VMAVASGGIH VWHMPALVEI FGDDSVLQFG GGTLGHPWGN APGATA NRV ALEACVQARN EGRNLAREGN DVIREAAKWS PELAVACELW KEIKFEFEAM DTV |
-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 |
-Image processing
Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 90012 |
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Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final 3D classification | Software - Name: RELION |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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