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Yorodumi- PDB-9enc: Human pseudouridine synthase 3 (PUS3 R116A mutant) and one tRNA-Gln -
+Open data
-Basic information
Entry | Database: PDB / ID: 9enc | ||||||||||||
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Title | Human pseudouridine synthase 3 (PUS3 R116A mutant) and one tRNA-Gln | ||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN / RNA modification / pseudouridylation / tRNA / homodimer | ||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | ||||||||||||
Authors | Lin, T.-Y. / Jezowski, J. / Glatt, S. | ||||||||||||
Funding support | Poland, European Union, Switzerland, 3items
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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. / Jezowski, J. / Glatt, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9enc.cif.gz | 171.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9enc.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 9enc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9enc_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 9enc_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 9enc_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 9enc_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/9enc ftp://data.pdbj.org/pub/pdb/validation_reports/en/9enc | HTTPS FTP |
-Related structure data
Related structure data | 19831 19830 19832 19833 19834 19835 19836 9enbC 9eneC 9enfC 9f9qC 16917 16926 M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 55639.102 Da / Num. of mol.: 2 / Mutation: R116A Source method: isolated from a genetically manipulated source Details: R116A single mutation / Source: (gene. exp.) Homo sapiens (human) / Gene: PUS3, FKSG32 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9BZE2, tRNA pseudouridine38/39 synthase #2: RNA chain | | Mass: 24047.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 0.14 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8393 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3010115 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265234 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |