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- EMDB-18601: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPD... -
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Open data
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Basic information
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Title | Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) ATP+GTP-bound form, less-compressed | |||||||||
![]() | RELION post-processed map | |||||||||
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![]() | Octamer / ATP+GTP complex / Purine metabolism / IMPDH / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||
![]() | Bulvas O / Kouba T / Pichova I | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: Mycobacterium smegmatis inosine monophosphate dehydrogenase (IMPDH) apo form Authors: Bulvas O / Kouba T / Pichova I | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 262.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 81.4 KB | ||
Masks | ![]() | 282.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 139 MB 225.1 MB 225.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qqqMC ![]() 17988 ![]() 18184 ![]() 18600 ![]() 18602 ![]() 18604 ![]() 18606 ![]() 18607 ![]() 18608 ![]() 8pw3C ![]() 8q65C ![]() 8qqpC ![]() 8qqrC ![]() 8qqtC ![]() 8qqvC ![]() 8qqwC ![]() 8qqxC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | RELION post-processed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8336 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Octameric assembly of inosine monophosphate dehydrogenase in comp...
Entire | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP+GTP |
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Components |
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-Supramolecule #1: Octameric assembly of inosine monophosphate dehydrogenase in comp...
Supramolecule | Name: Octameric assembly of inosine monophosphate dehydrogenase in complex with ATP+GTP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 426.658 KDa |
-Macromolecule #1: Inosine-5'-monophosphate dehydrogenase
Macromolecule | Name: Inosine-5'-monophosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: IMP dehydrogenase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 53.388988 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP ...String: MSIAESSVPI AVPVPTGGDD PTKVAMLGLT FDDVLLLPAA SDVVPATADT SSQLTKRIRL RVPLVSSAMD TVTESRMAIA MARAGGMGV LHRNLPVAEQ AGQVETVKRS EAGMVTDPVT CSPDNTLAEV DAMCARFRIS GLPVVDDTGE LVGIITNRDM R FEVDQSKP VSEVMTKAPL ITAKEGVSAE AALGLLRRHK IEKLPIVDGH GKLTGLITVK DFVKTEQFPL STKDSDGRLL VG AAVGVGD DAWTRAMTLV DAGVDVLIVD TAHAHNRGVL DMVSRLKQAV GERVDVVGGN VATRAAAAAL VEAGADAVKV GVG PGSICT TRVVAGVGAP QITAILEAVA ACKPYGVPVI ADGGLQYSGD IAKALAAGAS TAMLGSLLAG TAESPGELIF VNGK QFKSY RGMGSLGAMQ GRGAAKSYSK DRYFQDDVLS EDKLVPEGIE GRVPFRGPLG TVIHQLTGGL RAAMGYTGSA TIEQL QQAQ FVQITAAGLK ESHPHDITMT VEAPNYYTR UniProtKB: Inosine-5'-monophosphate dehydrogenase |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 16 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 149 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
Details: 50 mM HEPES (pH 7.5), 200 mM KCl, 5 mM DTT,4 mM MgCl2 Ligand: 0.5 mM ATP + 2 mM GTP + 1 mM IMP | ||||||||||||||||||||||||
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 40440 / Average exposure time: 2.0 sec. / Average electron dose: 44.0 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: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Details | Initial fitting was done in UCSF ChimeraX. Model refinement was done by iterative cycles of manual fitting with Coot and ISOLDE and automated fitting with phenix.real_space_refine. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 47.23 / Target criteria: CC coefficient |
Output model | ![]() PDB-8qqq: |