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Yorodumi- EMDB-14385: Cryo-EM structure of an a-carboxysome RuBisCO enzyme at 2.9 A res... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14385 | |||||||||
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Title | Cryo-EM structure of an a-carboxysome RuBisCO enzyme at 2.9 A resolution | |||||||||
Map data | Cryo-EM map of an a-carboxysome RuBisCO enzyme at 2.9 A resolution (D4 symmetry) | |||||||||
Sample |
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Keywords | Carboxysome / carbon fixation / cyanobacteria / PHOTOSYNTHESIS | |||||||||
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 | Cyanobium (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Mann D / Evans SL / Bergeron JRC | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Structure / Year: 2023 Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Authors: Sasha L Evans / Monsour M J Al-Hazeem / Daniel Mann / Nicolas Smetacek / Andrew J Beavil / Yaqi Sun / Taiyu Chen / Gregory F Dykes / Lu-Ning Liu / Julien R C Bergeron / Abstract: Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, ...Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14385.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-14385-v30.xml emd-14385.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14385_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_14385.png | 35.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14385 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14385 | HTTPS FTP |
-Validation report
Summary document | emd_14385_validation.pdf.gz | 441 KB | Display | EMDB validaton report |
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Full document | emd_14385_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | emd_14385_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_14385_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14385 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14385 | HTTPS FTP |
-Related structure data
Related structure data | 7yyoMC 8cmyC M: atomic model generated by this map C: citing same article (ref.) |
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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_14385.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map of an a-carboxysome RuBisCO enzyme at 2.9 A resolution (D4 symmetry) | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : RuBisCO
Entire | Name: RuBisCO |
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Components |
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-Supramolecule #1: RuBisCO
Supramolecule | Name: RuBisCO / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Cyanobium (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: Cyanobium (bacteria) |
Molecular weight | Theoretical: 52.526531 KDa |
Recombinant expression | Organism: Cyanobium (bacteria) |
Sequence | String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP ...String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAF YAFIAYPLDL FEEGSVTNVL TSLVGNVFGF KALRHLRLED IRFPMAFIKT CPGPPNGICV ERDRMNKYGR P LLGCTIKP KLGLSGKNYG RVVYECLRGG LDFTKDDENI NSQPFQRWQN RFEFVAEAVA LAQQETGEKK GHYLNCTAAT PE EMYERAE FAKELGQPII MHDYITGGFT ANTGLSKWCR KNGMLLHIHR AMHAVIDRHP KHGIHFRVLA KCLRLSGGDQ LHT GTVVGK LEGDRQTTLG FIDQLRESFI PEDRSRGNFF DQDWGSMPGV FAVASGGIHV WHMPALVAIF GDDSVLQFGG GTHG HPWGS AAGAAANRVA LEACVKARNA GREIEKESRD ILMEAAKHSP ELAIALETWK EIKFEFDTVD KLDVQ |
-Macromolecule #2: Ribulose bisphosphate carboxylase small chain
Macromolecule | Name: Ribulose bisphosphate carboxylase small 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: Cyanobium (bacteria) |
Molecular weight | Theoretical: 12.967611 KDa |
Recombinant expression | Organism: Cyanobium (bacteria) |
Sequence | String: MPFKSTVGDY QTVATLETFG FLPPMTQDEI YDQIAYIIAQ GWSPLIEHVH PSRSMATYWS YWKLPFFGEK DLGVIVSELE ACHRAYPDH HVRLVGYDAY TQSQGACFVV FEGR |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Macromolecule | Name: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: CAP |
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Molecular weight | Theoretical: 356.115 Da |
Chemical component information | ChemComp-CAP: |
-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) / Average electron dose: 30.0 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: 1.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |