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Yorodumi- EMDB-8692: Human Inosine Monophosphate Dehydrogenase 2 (hIMPDH2), Y12A mutant -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8692 | |||||||||
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Title | Human Inosine Monophosphate Dehydrogenase 2 (hIMPDH2), Y12A mutant | |||||||||
Map data | human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Kollman JK / Johnson MC / Burrell AL | |||||||||
Citation | Journal: Mol Biol Cell / Year: 2017 Title: Reconstituted IMPDH polymers accommodate both catalytically active and inactive conformations. Authors: Sajitha A Anthony / Anika L Burrell / Matthew C Johnson / Krisna C Duong-Ly / Yin-Ming Kuo / Jacqueline C Simonet / Peter Michener / Andrew Andrews / Justin M Kollman / Jeffrey R Peterson / Abstract: Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and ...Several metabolic enzymes undergo reversible polymerization into macromolecular assemblies. The function of these assemblies is often unclear but in some cases they regulate enzyme activity and metabolic homeostasis. The guanine nucleotide biosynthetic enzyme inosine monophosphate dehydrogenase (IMPDH) forms octamers that polymerize into helical chains. In mammalian cells, IMPDH filaments can associate into micron-length assemblies. Polymerization and enzyme activity are regulated in part by binding of purine nucleotides to an allosteric regulatory domain. ATP promotes octamer polymerization, whereas GTP promotes a compact, inactive conformation whose ability to polymerize is unknown. Also unclear is whether polymerization directly alters IMPDH catalytic activity. To address this, we identified point mutants of human IMPDH2 that either prevent or promote polymerization. Unexpectedly, we found that polymerized and non-assembled forms of recombinant IMPDH have comparable catalytic activity, substrate affinity, and GTP sensitivity and validated this finding in cells. Electron microscopy revealed that substrates and allosteric nucleotides shift the equilibrium between active and inactive conformations in both the octamer and the filament. Unlike other metabolic filaments, which selectively stabilize active or inactive conformations, recombinant IMPDH filaments accommodate multiple states. These conformational states are finely tuned by substrate availability and purine balance, while polymerization may allow cooperative transitions between states. | |||||||||
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_8692.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-8692-v30.xml emd-8692.xml | 7.9 KB 7.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8692_fsc.xml | 3.6 KB | Display | FSC data file |
Images | emd_8692.png | 182.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8692 | HTTPS FTP |
-Validation report
Summary document | emd_8692_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_8692_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_8692_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8692 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8692 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8692.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.52 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 : human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Entire | Name: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry |
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Components |
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-Supramolecule #1: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry
Supramolecule | Name: human inosine monophosphate dehydrogenase, Y12A mutant. D4 symmetry type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: BL21(DE3) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |