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- EMDB-44265: Apo Decameric Rubisco from Candidatus Methanofastidiosum methylth... -

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Basic information

Entry
Database: EMDB / ID: EMD-44265
TitleApo Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus
Map data
Sample
  • Complex: RUBISCO decamer
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION
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: 2.33 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: Apo Decameric Rubisco from Candidatus Methanofastidiosum methylthiophilus
Authors: Kaeser BP / Liu AK
History
DepositionMar 25, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_44265.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy EMDB: 0.3
Minimum - Maximum-1.9268351 - 3.1067357
Average (Standard dev.)0.00015454192 (±0.096077316)
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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Sample components

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Entire : RUBISCO decamer

EntireName: RUBISCO decamer
Components
  • Complex: RUBISCO decamer
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RUBISCO decamer

SupramoleculeName: RUBISCO decamer / 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: 10 / 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 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: 3903212
CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 882698
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 294232 / Software - Name: cryoSPARC

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