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- EMDB-43223: CABP-bound Decameric Rubisco from Candidatus Methanofastidiosum m... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-43223
TitleCABP-bound Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus
Map data
Sample
  • Complex: CABP-bound decameric RUBISCO
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: water
KeywordsCarboxylase / Oxygenase / LYASE
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / magnesium ion binding
Similarity search - Function
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
Similarity search - Component
Biological speciesCandidatus Methanofastidiosum methylthiophilus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsKaeser BP / Liu AK / Shih PM
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: CABP-bound Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus
Authors: Kaeser BP / Liu AK
History
DepositionDec 27, 2023-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43223.png

Downloads & links

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Map

FileDownload / File: emd_43223.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å		1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.3
Minimum - Maximum-1.9071419 - 3.1875882
Average (Standard dev.)-0.00040601828 (±0.08924537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43223_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_43223_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 : CABP-bound decameric RUBISCO

EntireName: CABP-bound decameric RUBISCO
Components
  • Complex: CABP-bound decameric RUBISCO
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: CABP-bound decameric RUBISCO

SupramoleculeName: CABP-bound decameric RUBISCO / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candidatus Methanofastidiosum methylthiophilus (archaea)

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Macromolecule #1: Ribulose bisphosphate carboxylase

MacromoleculeName: Ribulose bisphosphate carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Candidatus Methanofastidiosum methylthiophilus (archaea)
Molecular weightTheoretical: 52.86609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEKINETQLI KTLNIHQKGY VNFDLPNPKN GEYLLAVFHL ISGGKLNILQ AAAEVAAESS TGTNFNVNTE TPFSKEMNAV VYQIDLDQN LVWIAYPWRL FDRGGNVQNI LTYIVGNVLG MKEVSALKLL DVWFPPAMLE QYDGPSYTLD DMRKYLNVYD R PILGTIIK ...String:
MEKINETQLI KTLNIHQKGY VNFDLPNPKN GEYLLAVFHL ISGGKLNILQ AAAEVAAESS TGTNFNVNTE TPFSKEMNAV VYQIDLDQN LVWIAYPWRL FDRGGNVQNI LTYIVGNVLG MKEVSALKLL DVWFPPAMLE QYDGPSYTLD DMRKYLNVYD R PILGTIIK PKMGLTSAEY AEAAYDFWVG GGDFV(KCX)NDEP QANQDFCPYD KMVRNVKAAM DKAVKETGNK KVHSFNVS A ADFDTMIERC ELIRNAGFEP GSYAFLIDGI TAGWMAVQTL RRKYPDVFIH FHRAGHGSFT RPENPIGFSV LVLSKFARL AGASGIHTGT AGVGKMQGSP EEDVVAAQNI LRFKDKGHFF EQEWSKIFEG DKDAITIAQA DTARHVILED DSWRGVKKCC PIISGGLNP TLLKPFIDVM GNIDFITTMG AGCHAHPKGT TAGAKALVQA CEAYQKGIDI KEYAKTHKEL EEAIEFFTKK

UniProtKB: Ribulose bisphosphate carboxylase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 20 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

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

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 267 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4265503
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1554683
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 2 / Avg.num./class: 777342 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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