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- EMDB-50149: Myo-inositol-1-phosphate synthase from Thermochaetoides thermophi... -
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Open data
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Basic information
Entry | ![]() | |||||||||||||||
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Title | Myo-inositol-1-phosphate synthase from Thermochaetoides thermophila in complex with NAD | |||||||||||||||
![]() | Myo-inositol-1-phosphate synthase from Thermochaetoides thermophila; state 1 | |||||||||||||||
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![]() | inositol metabolism / endogenous / conformational selection / ISOMERASE | |||||||||||||||
Function / homology | ![]() inositol-3-phosphate synthase / inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||||||||
![]() | Traeger TK / Kyrilis FL / Hamdi F / Kastritis PL | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway Authors: Traeger TK / Kyrilis FL / Hamdi F / Kastritis PL | |||||||||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | |||
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f2kMC 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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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Myo-inositol-1-phosphate synthase from Thermochaetoides thermophila; state 1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.59 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Native homotetramer of the Myo-inositol-1-phosphate synthase
Entire | Name: Native homotetramer of the Myo-inositol-1-phosphate synthase |
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Components |
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-Supramolecule #1: Native homotetramer of the Myo-inositol-1-phosphate synthase
Supramolecule | Name: Native homotetramer of the Myo-inositol-1-phosphate synthase type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: inositol-3-phosphate synthase
Macromolecule | Name: inositol-3-phosphate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: inositol-3-phosphate synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 56.735477 KDa |
Sequence | String: IFKVNSPNVV YTDDEIRSKY VYRTTEVTTA EDGSLIATPR ETVYDFKVDR KLPKLGVMLV GWGGNNGSTI TAGIIANRRG LVWETRNGK QEANYYGSVI MGSTIKLGTD AKTHKDINIP FHSVLPMVHP NDIVIGGWDI SGLNLADAMD RAQVLEPSLK A LVRKEMAS ...String: IFKVNSPNVV YTDDEIRSKY VYRTTEVTTA EDGSLIATPR ETVYDFKVDR KLPKLGVMLV GWGGNNGSTI TAGIIANRRG LVWETRNGK QEANYYGSVI MGSTIKLGTD AKTHKDINIP FHSVLPMVHP NDIVIGGWDI SGLNLADAMD RAQVLEPSLK A LVRKEMAS MKPLPSIYYP DFIAANQEDR ADNILPGNKK CWEHVEEIRK NIRDFKAANG LDKVIVLWTA NTERYASIIE GV NDTADNL LNAIKNGHEE VSPSTVFAVS SILEGVPFIN GSPQNTFVPG CIELAERHGA FIGGDDFKSG QTKMKSALVD FLI NAGIKL TSIASYNHLG NNDGKNLSSQ RQFRSKEISK SNVVDDMVEA NTVLYKPGEH PDHIVVIKYV PAVGDSKRAM DEYH GEIFL GGHQTISIAN VCEDSLLASP LIIDLVIVAE LMTRIQWRLH KEDATEADWK YFHSVLSILS YMLKAPMTPP GTPVV NALA KQRAAMANIF RACLGLDPEN DMTLEHKLF UniProtKB: inositol-3-phosphate synthase |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 1 / 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 | particle |
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Sample preparation
Concentration | 0.6 mg/mL | ||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 400.0 kPa / Details: 15 mA | ||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: 6 s blot time with a blot force of -1. |
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Electron microscopy
Microscope | TFS GLACIOS |
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Temperature | Min: 77.15 K / Max: 103.15 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 6261 / Average electron dose: 28.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 240000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Local Installation |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-9f2k: |
-Atomic model buiding 2
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: Local Installation |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-9f2k: |