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- EMDB-15409: C1 Cyanobacteria sp PCC 7001 RuBisCO -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-15409
TitleC1 Cyanobacteria sp PCC 7001 RuBisCO
Map dataCryo-EM structure of an a-carboxysome RuBisCO enzyme with C1 symmetry at 3.8 A resolution
Sample
  • Complex: RuBisCO
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase, small subunitRuBisCO
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain ...Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase small subunit / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 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: To Be Published
Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact a-carboxysome
Authors: Evans SL / Al-Hazeem MJ / Mann D / Smetacek N / Beavil AJ / Sun Y / Chen T / Dykes GF / Liu L / Bergeron JRC
History
DepositionJul 18, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15409.png

Downloads & links

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Map

FileDownload / File: emd_15409.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of an a-carboxysome RuBisCO enzyme with C1 symmetry at 3.8 A resolution
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: 0.426
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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Half map: #2

Fileemd_15409_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15409_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RuBisCO

EntireName: RuBisCO
Components
  • Complex: RuBisCO
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase, small subunitRuBisCO
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RuBisCO

SupramoleculeName: RuBisCO / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)

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Macromolecule #1: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
Molecular weightTheoretical: 52.526531 KDa
SequenceString: 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

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Macromolecule #2: Ribulose bisphosphate carboxylase, small subunit

MacromoleculeName: Ribulose bisphosphate carboxylase, small subunit / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Cyanobium sp. PCC 7001 (bacteria)
Molecular weightTheoretical: 12.880533 KDa
SequenceString:
MPFKTVGDYQ TVATLETFGF LPPMTQDEIY DQIAYIIAQG WSPLIEHVHP SRSMATYWSY WKLPFFGEKD LGVIVSELEA CHRAYPDHH VRLVGYDAYT QSQGACFVVF EGR

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Macromolecule #3: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 7 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

ChemComp-CAP:
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131356
FSC plot (resolution estimation)

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