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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Human pseudouridine synthase 3 and tRNA-Gln | ||||||||||||
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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: 3.1 Å | ||||||||||||
![]() | Lin T-Y / Glatt S | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Human pseudouridine synthase 3 (PUS3) and tRNA-Gln Authors: Lin T-Y / Glatt S | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 70.4 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 875.2 KB | Display | ![]() |
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Full document | ![]() | 874.7 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8okdMC 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
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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
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : homodimer of PUS3 and tRNA-Gln complex
Entire | Name: homodimer of PUS3 and tRNA-Gln complex |
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Components |
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-Supramolecule #1: homodimer of PUS3 and tRNA-Gln complex
Supramolecule | Name: homodimer of PUS3 and tRNA-Gln complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 110 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-Gln
Supramolecule | Name: tRNA-Gln / 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 / Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.704199 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AMADNDTDRN QTEKLLKRVR ELEQEVQRLK KEQAKNKEDS NIRENSAGAG KTKRAFDFSA HGRRHVALRI AYMGWGYQGF ASQENTNNT IEEKLFEALT KTRLVESRQT SNYHRCGRTA KGVSAFGQVI SLDLRSQFPR GRDSEDFNVK EEANAAAEEI R YTHILNRV ...String: AMADNDTDRN QTEKLLKRVR ELEQEVQRLK KEQAKNKEDS NIRENSAGAG KTKRAFDFSA HGRRHVALRI AYMGWGYQGF ASQENTNNT IEEKLFEALT KTRLVESRQT SNYHRCGRTA KGVSAFGQVI SLDLRSQFPR GRDSEDFNVK EEANAAAEEI R YTHILNRV LPPDIRILAW APVEPSFSAR FSCLERTYRY FFPRADLDIV TMDYAAQKYV GTHDFRNLCK MDVANGVINF QR TILSAQV QLVGQSPGEG RWQEPFQLCQ FEVTGQAFLY HQVRCMMAIL FLIGQGMEKP EIIDELLNIE KNPQKPQYSM AVE FPLVLY DCKFENVKWI YDQEAQEFNI THLQQLWANH AVKTHMLYSM LQGLDTVPVP CGIGPKMDGM TEWGNVKPSV IKQT SAFVE GVKMRTYKPL MDRPKCQGLE SRIQHFVRRG RIEHPHLFHE EETKAKRDCN DTLEEENTNL ETPTKRVCVD TEIKS II UniProtKB: tRNA pseudouridine(38/39) synthase |
-Macromolecule #2: human tRNA-Gln (70-MER)
Macromolecule | Name: human tRNA-Gln (70-MER) / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.047236 KDa |
Sequence | String: GGCCCCAUGG UGUAAUGGUU AGCACUCUGG ACUUUGAAUC CAGCGAUCCG AGUUCAAAUC UCGGUGGGAC CUCCA |
-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 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 8 mA |
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: 8320 / 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: 1.8 µm / Nominal defocus min: 0.9 µm |
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 | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-8okd: |