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Yorodumi- EMDB-12731: Structure of the repeat unit in the network formed by CcmM full l... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12731 | |||||||||
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Title | Structure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus | |||||||||
Map data | Structure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus | |||||||||
Sample |
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Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / monooxygenase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Zang K / Huping W / Ulrich FH / Manajit HH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2021 Title: Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis. Authors: Kun Zang / Huping Wang / F Ulrich Hartl / Manajit Hayer-Hartl / Abstract: Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural ...Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation. | |||||||||
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_12731.map.gz | 11.8 MB | EMDB map data format | |
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Header (meta data) | emd-12731-v30.xml emd-12731.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_12731.png | 36.8 KB | ||
Others | emd_12731_additional_1.map.gz | 13.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12731 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12731 | HTTPS FTP |
-Validation report
Summary document | emd_12731_validation.pdf.gz | 325.7 KB | Display | EMDB validaton report |
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Full document | emd_12731_full_validation.pdf.gz | 325.3 KB | Display | |
Data in XML | emd_12731_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | emd_12731_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12731 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12731 | HTTPS FTP |
-Related 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_12731.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the repeat unit in the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.885 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: EM map sharpen by DeepEMhancer
File | emd_12731_additional_1.map | ||||||||||||
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Annotation | EM map sharpen by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the network formed by CcmM full length isoform and Rubisco from S...
Entire | Name: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus |
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Components |
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-Supramolecule #1: the network formed by CcmM full length isoform and Rubisco from S...
Supramolecule | Name: the network formed by CcmM full length isoform and Rubisco from Synechococcus elongatus type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-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 | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 698820 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |