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Yorodumi- EMDB-14623: Subtomogram averaging of Rubisco from Cyanobium carboxysome (inne... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14623 | ||||||||||||
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Title | Subtomogram averaging of Rubisco from Cyanobium carboxysome (innermost layer) | ||||||||||||
Map data | |||||||||||||
Sample |
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Biological species | Cyanobium sp. PCC 7001 (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.8 Å | ||||||||||||
Authors | Ni T / Seaton-Burn W / Zhu Y / Zhang P | ||||||||||||
Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure and assembly of cargo Rubisco in two native α-carboxysomes. Authors: Tao Ni / Yaqi Sun / Will Burn / Monsour M J Al-Hazeem / Yanan Zhu / Xiulian Yu / Lu-Ning Liu / Peijun Zhang / Abstract: Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase ...Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14623.map.gz | 32.1 MB | EMDB map data format | |
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Header (meta data) | emd-14623-v30.xml emd-14623.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14623_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_14623.png | 130.7 KB | ||
Masks | emd_14623_msk_1.map | 34.3 MB | Mask map | |
Others | emd_14623_half_map_1.map.gz emd_14623_half_map_2.map.gz | 20.2 MB 20.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14623 | HTTPS FTP |
-Validation report
Summary document | emd_14623_validation.pdf.gz | 871.4 KB | Display | EMDB validaton report |
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Full document | emd_14623_full_validation.pdf.gz | 871 KB | Display | |
Data in XML | emd_14623_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_14623_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14623 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14623.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14623_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: emClarity half map 1 from cisTEM reconstruction
File | emd_14623_half_map_1.map | ||||||||||||
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Annotation | emClarity half map 1 from cisTEM reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: emClarity half map 2 from cisTEM reconstruction
File | emd_14623_half_map_2.map | ||||||||||||
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Annotation | emClarity half map 2 from cisTEM reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rubisco from Cyanobium carboxysome (innermost layer)
Entire | Name: Rubisco from Cyanobium carboxysome (innermost layer) |
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Components |
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-Supramolecule #1: Rubisco from Cyanobium carboxysome (innermost layer)
Supramolecule | Name: Rubisco from Cyanobium carboxysome (innermost layer) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
-Macromolecule #1: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large s...
Macromolecule | Name: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
Sequence | String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDL DFYKGRCYRI EDVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF K ALRHLRLE DIRFPMAFIK TCPGPPNGIC VERDRMNKYG RPLLGCTIKP ...String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDL DFYKGRCYRI EDVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF K ALRHLRLE DIRFPMAFIK TCPGPPNGIC VERDRMNKYG RPLLGCTIKP KLGLSGKNYG RV VYECLRG GLDFTKDDEN INSQPFQRWQ NRFEFVAEAV ALAQQETGEK KGHYLNCTAA TPE EMYERA EFAKELGQPI IMHDYITGGF TANTGLSKWC RKNGMLLHIH RAMHAVIDRH PKHG IHFRV LAKCLRLSGG DQLHTGTVVG KLEGDRQTTL GFIDQLRESF IPEDRSRGNF FDQDW GSMP GVFAVASGGI HVWHMPALVA IFGDDSVLQF GGGTHGHPWG SAAGAAANRV ALEACV KAR NAGREIEKES RDILMEAAKH SPELAIALET WKEIKFEFDT VDKLDVQ |
-Macromolecule #2: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small s...
Macromolecule | Name: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
Sequence | String: MPFKSTVGDY QTVATLETFG FLPPMTQDEI YDQIAYIIAQ GWSPLIEHVH PSRSMATYWS YWKLPFFGE KDLGVIVSEL EACHRAYPDH HVRLVGYDAY TQSQGACFVV FEGR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.65 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |