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- EMDB-1678: CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase B... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1678 | |||||||||
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Title | CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP | |||||||||
![]() | CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP | |||||||||
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![]() | AAA+ atpase / metallation / tetrapyrroles | |||||||||
Function / homology | ![]() bacteriochlorophyll biosynthetic process / magnesium chelatase / magnesium chelatase activity / photosynthesis / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.0 Å | |||||||||
![]() | Lundqvist J / Elmlund H / Peterson-Wulff R / Elmlund D / Emanuelsson C / Hebert H / Willows R / Hansson M / Lindahl M / Al-Karadaghi S | |||||||||
![]() | ![]() Title: ATP-induced conformational dynamics in the AAA+ motor unit of magnesium chelatase. Authors: Joakim Lundqvist / Hans Elmlund / Ragna Peterson Wulff / Lisa Berglund / Dominika Elmlund / Cecilia Emanuelsson / Hans Hebert / Robert D Willows / Mats Hansson / Martin Lindahl / Salam Al-Karadaghi / ![]() Abstract: Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using ...Mg-chelatase catalyzes the first committed step of the chlorophyll biosynthetic pathway, the ATP-dependent insertion of Mg(2+) into protoporphyrin IX (PPIX). Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 A, 14 A, and 13 A resolution, respectively. We show that the two AAA+ modules of the subunits form a unique complex of 3 dimers related by a three-fold axis. The reconstructions demonstrate substantial differences between the conformations of the complex in the presence of ATP and ADP, and suggest that the C-terminal integrin-I domains of the BchD subunits play a central role in transmitting conformational changes of BchI to BchD. Based on these data a model for the function of magnesium chelatase is proposed. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.7 KB 8.7 KB | Display Display | ![]() |
Images | ![]() | 29.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 201.7 KB | Display | ![]() |
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Full document | ![]() | 200.9 KB | Display | |
Data in XML | ![]() | 4.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2x31MC ![]() 1676C ![]() 1677C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoEM 3D reconstruction of Rhodobacter capsulatus Mg-chelatase BchID complex in the presence of AMPPNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
Entire | Name: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP |
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Components |
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-Supramolecule #1000: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP
Supramolecule | Name: Complex of Mg-chelatase subunits BchI and BchD in presence of AMPPNP type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Theoretical: 660 KDa |
-Macromolecule #1: Biosynthetic enzyme
Macromolecule | Name: Biosynthetic enzyme / type: protein_or_peptide / ID: 1 / Name.synonym: Mg chelatase / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 660 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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Electron microscopy
Microscope | JEOL 2010F |
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Image recording | Digitization - Scanner: ZEISS SCAI / Number real images: 6 |
Electron beam | Acceleration voltage: 120 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 60000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
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Image processing
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 17623 |
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Final two d classification | Number classes: 526 |