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Yorodumi- EMDB-14376: Cryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14376 | |||||||||
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Title | Cryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry | |||||||||
Map data | Cryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry | |||||||||
Sample |
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Biological species | Cyanobium sp. PCC 7001 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Evans SL / Mann D / 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_14376.map.gz | 59.6 MB | EMDB map data format | |
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Header (meta data) | emd-14376-v30.xml emd-14376.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14376_fsc.xml | 8.5 KB | Display | FSC data file |
Images | emd_14376.png | 59.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14376 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14376 | HTTPS FTP |
-Validation report
Summary document | emd_14376_validation.pdf.gz | 547.3 KB | Display | EMDB validaton report |
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Full document | emd_14376_full_validation.pdf.gz | 546.8 KB | Display | |
Data in XML | emd_14376_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_14376_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14376 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14376 | 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_14376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
-Macromolecule #1: CbbL
Macromolecule | Name: CbbL / 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 VWSELLVDLD FYKGRCYRIE DVPGDKEAFY AFIAYPLDLF EEGSVTNVLT SLVGNVFGFK ALRHLRLEDI RFPMAFIKTC PGPPNGICVE RDRMNKYGRP LLGCTIKPKL ...String: MSKKYDAGVK EYRDTYWTPD YVPLDTDLLA CFKCTGQEGV PKEEVAAAVA AESSTGTWST VWSELLVDLD FYKGRCYRIE DVPGDKEAFY AFIAYPLDLF EEGSVTNVLT SLVGNVFGFK ALRHLRLEDI RFPMAFIKTC PGPPNGICVE RDRMNKYGRP LLGCTIKPKL GLSGKNYGRV VYECLRGGLD FTKDDENINS QPFQRWQNRF EFVAEAVALA QQETGEKKGH YLNCTAATPE EMYERAEFAK ELGQPIIMHD YITGGFTANT GLSKWCRKNG MLLHIHRAMH AVIDRHPKHG IHFRVLAKCL RLSGGDQLHT GTVVGKLEGD RQTTLGFIDQ LRESFIPEDR SRGNFFDQDW GSMPGVFAVA SGGIHVWHMP ALVAIFGDDS VLQFGGGTHG HPWGSAAGAA ANRVALEACV KARNAGREIE KESRDILMEA AKHSPELAIA LETWKEIKFE FDTVDKLDVQ |
-Macromolecule #2: CbbS
Macromolecule | Name: CbbS / 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 YWKLPFFGEK DLGVIVSELE ACHRAYPDHH VRLVGYDAYT QSQGACFVVF EGR |
-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 |