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Yorodumi- EMDB-14590: Subtomogram averaging of Rubisco from native Halothiobacillus car... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14590 | ||||||||||||
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Title | Subtomogram averaging of Rubisco from native Halothiobacillus carboxysomes | ||||||||||||
Map data | final merged map | ||||||||||||
Sample |
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Keywords | Rubisco / carboxysome / UNKNOWN FUNCTION | ||||||||||||
Function / homology | Function and homology information carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | ||||||||||||
Biological species | Halothiobacillus neapolitanus (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Ni T / Zhu Y / Yu X / Sun Y / Liu L / Zhang P | ||||||||||||
Funding support | European Union, United Kingdom, 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. #1: Journal: bioRxiv / Year: 2022 Title: Tales of Two alpha Carboxysomes the Structure and Assembly of Cargo Rubisco Authors: Ni T / Sun Y / Seaton-Burn W / AI-Hazeem M / Zhu Y / Yu X / Liu L / Zhang P | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14590.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-14590-v30.xml emd-14590.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14590_fsc.xml | 36.6 KB | Display | FSC data file |
Images | emd_14590.png | 198.6 KB | ||
Filedesc metadata | emd-14590.cif.gz | 5.9 KB | ||
Others | emd_14590_half_map_1.map.gz emd_14590_half_map_2.map.gz | 19.4 MB 19.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14590 | HTTPS FTP |
-Validation report
Summary document | emd_14590_validation.pdf.gz | 837.5 KB | Display | EMDB validaton report |
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Full document | emd_14590_full_validation.pdf.gz | 837.1 KB | Display | |
Data in XML | emd_14590_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | emd_14590_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14590 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14590 | HTTPS FTP |
-Related structure data
Related structure data | 7zbtMC 7zc1C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14590.map.gz / Format: CCP4 / Size: 21.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | final merged map | ||||||||||||||||||||
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
-Half map: half map 2
File | emd_14590_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_14590_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : alpha carboxysomes
Entire | Name: alpha carboxysomes |
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Components |
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-Supramolecule #1: alpha carboxysomes
Supramolecule | Name: alpha carboxysomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Halothiobacillus neapolitanus (bacteria) |
-Macromolecule #1: Ribulose bisphosphate carboxylase large chain
Macromolecule | Name: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase |
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Source (natural) | Organism: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2 |
Molecular weight | Theoretical: 52.7025 KDa |
Recombinant expression | Organism: Halothiobacillus neapolitanus (bacteria) |
Sequence | String: MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTDM DYYKGRAYRI EDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG FKAVRGLRLE DVRFPLAYVK TCGGPPHGIQ VERDKMNKYG R PLLGCTIK ...String: MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTDM DYYKGRAYRI EDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG FKAVRGLRLE DVRFPLAYVK TCGGPPHGIQ VERDKMNKYG R PLLGCTIK PKLGLSAKNY GRAVYECLRG GLDFTKDDEN INSQPFMRWR DRFLFVQDAT ETAEAQTGER KGHYLNVTAP TP EEMYKRA EFAKEIGAPI IMHDYITGGF TANTGLAKWC QDNGVLLHIH RAMHAVIDRN PNHGIHFRVL TKILRLSGGD HLH TGTVVG KLEGDRASTL GWIDLLRESF IPEDRSRGIF FDQDWGSMPG VFAVASGGIH VWHMPALVNI FGDDSVLQFG GGTL GHPWG NAAGAAANRV ALEACVEARN QGRDIEKEGK EILTAAAQHS PELKIAMETW KEIKFEFDTV DKLDTQNR UniProtKB: Ribulose bisphosphate carboxylase large chain |
-Macromolecule #2: Ribulose bisphosphate carboxylase small subunit
Macromolecule | Name: Ribulose bisphosphate carboxylase small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Halothiobacillus neapolitanus (bacteria) / Strain: ATCC 23641 / c2 |
Molecular weight | Theoretical: 12.866575 KDa |
Recombinant expression | Organism: Halothiobacillus neapolitanus (bacteria) |
Sequence | String: MAEMQDYKQS LKYETFSYLP PMNAERIRAQ IKYAIAQGWS PGIEHVEVKN SMNQYWYMWK LPFFGEQNVD NVLAEIEACR SAYPTHQVK LVAYDNYAQS LGLAFVVYRG N UniProtKB: Ribulose bisphosphate carboxylase small subunit |
-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 K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 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: 6.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |