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- EMDB-19832: Human pseudouridine synthase 3 (PUS3 D118A mutant) and two tRNA-Arg -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Human pseudouridine synthase 3 (PUS3 D118A mutant) and two tRNA-Arg | ||||||||||||
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![]() | RNA modification / pseudouridylation / tRNA / homodimer / RNA BINDING PROTEIN | ||||||||||||
Function / homology | ![]() tRNA pseudouridine38/39 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / tRNA modification / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||||||||
![]() | Lin T-Y / Jezowski J / Glatt S | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The molecular basis of tRNA selectivity by human pseudouridine synthase 3 (PUS3) Authors: Lin T-Y / Jezowski J / Glatt S | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 62.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 102.9 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 872.1 KB | Display | ![]() |
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Full document | ![]() | 871.7 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9eneMC ![]() 19830 ![]() 19831 ![]() 19833 ![]() 19834 ![]() 19835 ![]() 19836 ![]() 9enbC ![]() 9encC ![]() 9enfC ![]() 9f9qC ![]() 16917 ![]() 16926 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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Voxel size | X=Y=Z: 0.86 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 : Homodimer of human PUS3 and two tRNA-Arg
Entire | Name: Homodimer of human PUS3 and two tRNA-Arg |
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Components |
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-Supramolecule #1: Homodimer of human PUS3 and two tRNA-Arg
Supramolecule | Name: Homodimer of human PUS3 and two tRNA-Arg / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 160 KDa |
-Supramolecule #2: Pseudouridine synthase 3 (PUS3)
Supramolecule | Name: Pseudouridine synthase 3 (PUS3) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: tRNA-Arg
Supramolecule | Name: tRNA-Arg / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: tRNA pseudouridine(38/39) synthase
Macromolecule | Name: tRNA pseudouridine(38/39) synthase / type: protein_or_peptide / ID: 1 / Details: D118A single mutation / Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.681207 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL ...String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL PPDIRILAWA PVEPSFSARF SCLERTYRYF FPRADLDIVT MDYAAQKYVG THDFRNLCKM DVANGVINFQ RT ILSAQVQ LVGQSPGEGR WQEPFQLCQF EVTGQAFLYH QVRCMMAILF LIGQGMEKPE IIDELLNIEK NPQKPQYSMA VEF PLVLYD CKFENVKWIY DQEAQEFNIT HLQQLWANHA VKTHMLYSML QGLDTVPVPC GIGPKMDGMT EWGNVKPSVI KQTS AFVEG VKMRTYKPLM DRPKCQGLES RIQHFVRRGR IEHPHLFHEE ETKAKRDCND TLEEENTNLE TPTKRVCVDT EIKSI I UniProtKB: tRNA pseudouridine(38/39) synthase |
-Macromolecule #2: tRNA-Arg
Macromolecule | Name: tRNA-Arg / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.472488 KDa |
Sequence | String: GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAAUU CAAAGGUUGU GGGUUCGAGU CCCACCAGAG UCGCCA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / 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 grids imaged: 1 / Number real images: 8736 / Average electron dose: 40.0 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: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / 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 | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-9ene: |