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- EMDB-20706: Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free inte... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20706 | |||||||||
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Title | Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free interfacial octamer reconstruction. | |||||||||
![]() | Human IMPDH2 treated with ATP, IMP, NAD , and 2 mM GTP. Free interfacial octamer reconstruction. | |||||||||
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![]() | metabolism / filament / allostery / adenine / guanine / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | ![]() 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 ...'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / lymphocyte proliferation / IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / Azathioprine ADME / peroxisomal membrane / GTP biosynthetic process / cellular response to interleukin-4 / circadian rhythm / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / nucleotide binding / Neutrophil degranulation / DNA binding / RNA binding / extracellular exosome / extracellular region / metal ion binding / nucleus / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.79 Å | |||||||||
![]() | Johnson MC / Kollman JM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. Authors: Johnson MC / Kollman JM | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 92 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 45.7 MB 45.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 846.7 KB | Display | ![]() |
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Full document | ![]() | 846.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ua5MC ![]() 6uajMC ![]() 6u8eC ![]() 6u8nC ![]() 6u8rC ![]() 6u8sC ![]() 6u9oC ![]() 6ua2C ![]() 6ua4C ![]() 6uc2C ![]() 6udoC ![]() 6udpC ![]() 6udqC 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 | Human IMPDH2 treated with ATP, IMP, NAD , and 2 mM GTP. Free interfacial octamer reconstruction. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free inte...
Entire | Name: Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free interfacial octamer reconstruction. |
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Components |
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-Supramolecule #1: Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free inte...
Supramolecule | Name: Human IMPDH2 treated with ATP, IMP, NAD+, and 2 mM GTP. Free interfacial octamer reconstruction. type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Inosine-5'-monophosphate dehydrogenase 2
Macromolecule | Name: Inosine-5'-monophosphate dehydrogenase 2 / 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: 56.4805 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI ...String: SEFELMADYL ISGGTSYVPD DGLTAQQLFN CGDGLTYNDF LILPGYIDFT ADQVDLTSAL TKKITLKTPL VSSPMDTVTE AGMAIAMAL TGGIGFIHHN CTPEFQANEV RKVKKYEQGF ITDPVVLSPK DRVRDVFEAK ARHGFCGIPI TDTGRMGSRL V GIISSRDI DFLKEEEHDC FLEEIMTKRE DLVVAPAGIT LKEANEILQR SKKGKLPIVN EDDELVAIIA RTDLKKNRDY PL ASKDAKK QLLCGAAIGT HEDDKYRLDL LAQAGVDVVV LDSSQGNSIF QINMIKYIKD KYPNLQVIGG NVVTAAQAKN LID AGVDAL RVGMGSGSIC ITQEVLACGR PQATAVYKVS EYARRFGVPV IADGGIQNVG HIAKALALGA STVMMGSLLA ATTE APGEY FFSDGIRLKK YRGMGSLDAM DKHLSSQNRY FSEADKIKVA QGVSGAVQDK GSIHKFVPYL IAGIQHSCQD IGAKS LTQV RAMMYSGELK FEKRTSSAQV EGGVHSLHSY EKRLF UniProtKB: Inosine-5'-monophosphate dehydrogenase 2 |
-Macromolecule #2: INOSINIC ACID
Macromolecule | Name: INOSINIC ACID / type: ligand / ID: 2 / Number of copies: 8 / Formula: IMP |
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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 |
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Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ![]() ChemComp-NAD: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |