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Yorodumi- EMDB-19830: Human pseudouridine synthase 3 (PUS3 R116A mutant) and two tRNA-Gln -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19830 | ||||||||||||
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Title | Human pseudouridine synthase 3 (PUS3 R116A mutant) and two tRNA-Gln | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | RNA modification / pseudouridylation / tRNA / homodimer / RNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | ||||||||||||
Authors | Lin T-Y / Jezowski J / Glatt S | ||||||||||||
Funding support | Poland, European Union, Switzerland, 3 items
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Citation | Journal: Mol.Cell Title: The molecular basis of tRNA selectivity by human pseudouridine synthase 3 (PUS3) Authors: Lin T-Y / Koziej L / Glatt S | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19830.map.gz | 62.5 MB | EMDB map data format | |
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Header (meta data) | emd-19830-v30.xml emd-19830.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19830_fsc.xml | 10.5 KB | Display | FSC data file |
Images | emd_19830.png | 103.3 KB | ||
Filedesc metadata | emd-19830.cif.gz | 6.4 KB | ||
Others | emd_19830_half_map_1.map.gz emd_19830_half_map_2.map.gz | 115.8 MB 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19830 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19830 | HTTPS FTP |
-Validation report
Summary document | emd_19830_validation.pdf.gz | 881.2 KB | Display | EMDB validaton report |
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Full document | emd_19830_full_validation.pdf.gz | 880.8 KB | Display | |
Data in XML | emd_19830_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_19830_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19830 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19830 | HTTPS FTP |
-Related structure data
Related structure data | 9enbMC 19831 19832 19833 19834 19835 19836 9encC 9eneC 9enfC 9f9qC 16917 16926 M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19830.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8456 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Homodimer of human PUS3 and two tRNA-Gln
Entire | Name: Homodimer of human PUS3 and two tRNA-Gln |
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Components |
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-Supramolecule #1: Homodimer of human PUS3 and two tRNA-Gln
Supramolecule | Name: Homodimer of human PUS3 and two tRNA-Gln / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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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: Homo sapiens (human) |
-Supramolecule #3: tRNA-Gln
Supramolecule | Name: tRNA-Gln / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: tRNA pseudouridine(38/39) synthase
Macromolecule | Name: tRNA pseudouridine(38/39) synthase / type: protein_or_peptide / ID: 1 / Details: R116A single mutation / Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 55.639102 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGATDK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL ...String: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGATDK 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-Gln
Macromolecule | Name: tRNA-Gln / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.047236 KDa |
Sequence | String: GGCCCCAUGG UGUAAUGGUU AGCACUCUGG ACUUUGAAUC CAGCGAUCCG AGUUCAAAUC UCGGUGGGAC CUCCA |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 8393 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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 |
+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-9enb: |