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- EMDB-14376: Cryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at... -

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Basic information

Entry
Database: EMDB / ID: EMD-14376
TitleCryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry
Map dataCryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry
Sample
  • Complex: RuBisCO
    • Protein or peptide: CbbL
    • Protein or peptide: CbbS
Biological speciesCyanobium sp. PCC 7001 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsEvans SL / Mann D / Bergeron JRC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: 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
DepositionFeb 17, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14376.png

Downloads & links

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Map

FileDownload / File: emd_14376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the Cyanobium sp. PCC 7001 RuBisCO enzyme at 3.8 A resolution with C1 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å		1.11 Å/pix.
x 256 pix.
= 284.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-0.8033051 - 2.1630597
Average (Standard dev.)0.019220717 (±0.11416591)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 284.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : RuBisCO

EntireName: RuBisCO
Components
  • Complex: RuBisCO
    • Protein or peptide: CbbL
    • Protein or peptide: CbbS

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Supramolecule #1: RuBisCO

SupramoleculeName: RuBisCO / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)

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Macromolecule #1: CbbL

MacromoleculeName: CbbL / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString: 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

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Macromolecule #2: CbbS

MacromoleculeName: CbbS / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
SequenceString:
MPFKSTVGDY QTVATLETFG FLPPMTQDEI YDQIAYIIAQ GWSPLIEHVH PSRSMATYWS YWKLPFFGEK DLGVIVSELE ACHRAYPDHH VRLVGYDAYT QSQGACFVVF EGR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131356
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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