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Yorodumi- EMDB-2069: Octameric structure of IMPDH from Pseudomonas aeruginosa in its A... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2069 | |||||||||
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Title | Octameric structure of IMPDH from Pseudomonas aeruginosa in its APO form | |||||||||
Map data | Cryo-EM map of IMPDH from Pseudomonas Aeruginosa at 15.5A resolution in its APO conformation | |||||||||
Sample |
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Keywords | IMPDH / nucleotide metabolism / CBS domains | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.5 Å | |||||||||
Authors | Labesse G / Vaupre L / Salard-Arnaud I / Alexandre T / Lai Kee Him J / Raynal B / Bron P / Munier-Lehmann H | |||||||||
Citation | Journal: Structure / Year: 2013 Title: MgATP regulates allostery and fiber formation in IMPDHs. Authors: Gilles Labesse / Thomas Alexandre / Laurène Vaupré / Isabelle Salard-Arnaud / Joséphine Lai Kee Him / Bertrand Raynal / Patrick Bron / Hélène Munier-Lehmann / Abstract: Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in nucleotide biosynthesis studied as an important therapeutic target and its complex functioning in vivo is still puzzling ...Inosine-5'-monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in nucleotide biosynthesis studied as an important therapeutic target and its complex functioning in vivo is still puzzling and debated. Here, we highlight the structural basis for the regulation of IMPDHs by MgATP. Our results demonstrate the essential role of the CBS tandem, conserved among almost all IMPDHs. We found that Pseudomonas aeruginosa IMPDH is an octameric enzyme allosterically regulated by MgATP and showed that this octameric organization is widely conserved in the crystal structures of other IMPDHs. We also demonstrated that human IMPDH1 adopts two types of complementary octamers that can pile up into isolated fibers in the presence of MgATP. The aggregation of such fibers in the autosomal dominant mutant, D226N, could explain the onset of the retinopathy adRP10. Thus, the regulatory CBS modules in IMPDHs are functional and they can either modulate catalysis or macromolecular assembly. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2069.map.gz | 8.1 MB | EMDB map data format | |
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Header (meta data) | emd-2069-v30.xml emd-2069.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_2069.png | 114.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2069 | HTTPS FTP |
-Validation report
Summary document | emd_2069_validation.pdf.gz | 190 KB | Display | EMDB validaton report |
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Full document | emd_2069_full_validation.pdf.gz | 189.1 KB | Display | |
Data in XML | emd_2069_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2069 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2069 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2069.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of IMPDH from Pseudomonas Aeruginosa at 15.5A resolution in its APO conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : IMPDH apo filtered at 15.5 A resolution from Pseudomonas aeruginosa
Entire | Name: IMPDH apo filtered at 15.5 A resolution from Pseudomonas aeruginosa |
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Components |
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-Supramolecule #1000: IMPDH apo filtered at 15.5 A resolution from Pseudomonas aeruginosa
Supramolecule | Name: IMPDH apo filtered at 15.5 A resolution from Pseudomonas aeruginosa type: sample / ID: 1000 / Oligomeric state: octameric / Number unique components: 1 |
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Molecular weight | Theoretical: 430 KDa |
-Macromolecule #1: Inosine-5'-monophosphate dehydrogenase
Macromolecule | Name: Inosine-5'-monophosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Name.synonym: IMPDH / Number of copies: 8 / Oligomeric state: octamer / Recombinant expression: Yes |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) / synonym: Bacteria |
Molecular weight | Theoretical: 430 KDa |
Recombinant expression | Organism: Bacteria (eubacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 20 mM potassium phosphate pH 8 and 0.1 M KCl |
Grid | Details: Quantifoil R2.2, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 102.15 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 1 second |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 93.15 K / Max: 96.15 K / Average: 95.15 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Specialist optics | Energy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | Weak beam illumination |
Date | Oct 1, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Number real images: 74 / Average electron dose: 18 e/Å2 Details: Images recorded with the 4K X 4K slow-scan CCD camera (Gatan inc.), which explains why the nominal magnification is 100000 and 130137 when calibrated on the camera. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 130137 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 100000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected using an semi-automatic selection program (boxer) |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC, FREALIGN / Number images used: 10625 |