[English] 日本語
![](img/lk-miru.gif)
- EMDB-42029: Human retinal variant phosphomimetic IMPDH1(546)-S477D filament b... -
+
Open data
-
Basic information
Entry | ![]() | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human retinal variant phosphomimetic IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+, interface-centered | ||||||||||||||||||
![]() | Sharpened map from CryoSPARC | ||||||||||||||||||
![]() |
| ||||||||||||||||||
![]() | dehydrogenase / nucleotide synthesis / filament / phosphomimetic / OXIDOREDUCTASE | ||||||||||||||||||
Function / homology | ![]() Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / azurophil granule lumen / Potential therapeutics for SARS / secretory granule lumen / nucleic acid binding ...Purine ribonucleoside monophosphate biosynthesis / IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / Azathioprine ADME / GTP biosynthetic process / azurophil granule lumen / Potential therapeutics for SARS / secretory granule lumen / nucleic acid binding / ficolin-1-rich granule lumen / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular region / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||||||||||||||
![]() | Calise SJ / Kollman JM | ||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||
![]() | ![]() Title: Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. Authors: S John Calise / Audrey G O'Neill / Anika L Burrell / Miles S Dickinson / Josephine Molfino / Charlie Clarke / Joel Quispe / David Sokolov / Rubén M Buey / Justin M Kollman / ![]() ![]() Abstract: Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback ...Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased. | ||||||||||||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 229.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
Images | ![]() | 164.1 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 225.4 MB 225.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u8yMC ![]() 8u7mC ![]() 8u7qC ![]() 8u7vC ![]() 8u8oC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map from CryoSPARC | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.843 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half map 1
File | emd_42029_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map 2
File | emd_42029_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+
Entire | Name: IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+ |
---|---|
Components |
|
-Supramolecule #1: IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+
Supramolecule | Name: IMPDH1(546)-S477D filament bound by ATP, IMP, and NAD+ type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 468 KDa |
-Macromolecule #1: Inosine-5'-monophosphate dehydrogenase 1
Macromolecule | Name: Inosine-5'-monophosphate dehydrogenase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: IMP dehydrogenase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 58.542906 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GSMADYLISG GTGYVPEDGL TAQQLFASAD GLTYNDFLIL PGFIDFIADE VDLTSALTRK ITLKTPLISS PMDTVTEADM AIAMALMGG IGFIHHNCTP EFQANEVRKV KKFEQGFITD PVVLSPSHTV GDVLEAKMRH GFSGIPITET GTMGSKLVGI V TSRDIDFL ...String: GSMADYLISG GTGYVPEDGL TAQQLFASAD GLTYNDFLIL PGFIDFIADE VDLTSALTRK ITLKTPLISS PMDTVTEADM AIAMALMGG IGFIHHNCTP EFQANEVRKV KKFEQGFITD PVVLSPSHTV GDVLEAKMRH GFSGIPITET GTMGSKLVGI V TSRDIDFL AEKDHTTLLS EVMTPRIELV VAPAGVTLKE ANEILQRSKK GKLPIVNDCD ELVAIIARTD LKKNRDYPLA SK DSQKQLL CGAAVGTRED DKYRLDLLTQ AGVDVIVLDS SQGNSVYQIA MVHYIKQKYP HLQVIGGNVV TAAQAKNLID AGV DGLRVG MGCGSICITQ EVMACGRPQG TAVYKVAEYA RRFGVPIIAD GGIQTVGHVV KALALGASTV MMGSLLAATT EAPG EYFFS DGVRLKKYRG MGSLDAMEKS SSSQKRYFSE GDKVKIAQGV SGSIQDKGSI QKFVPYLIAG IQHGCQDIGA RSLDV LRSM MYSGELKFEK RTMSAQIEGG VHGLHSYTFL PFTKSGCTED SGGGRGGGGD APQCPLLGTA SLHN UniProtKB: Inosine-5'-monophosphate dehydrogenase 1 |
-Macromolecule #2: INOSINIC ACID
Macromolecule | Name: INOSINIC ACID / type: ligand / ID: 2 / Number of copies: 8 / Formula: IMP |
---|---|
Molecular weight | Theoretical: 348.206 Da |
Chemical component information | ![]() ChemComp-I: |
-Macromolecule #3: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAD |
---|---|
Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | filament |
-
Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: C-flat-2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Number real images: 4632 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |