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- PDB-9ene: Human pseudouridine synthase 3 (PUS3 D118A mutant) and two tRNA-Arg -

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Basic information

Entry
Database: PDB / ID: 9ene
TitleHuman pseudouridine synthase 3 (PUS3 D118A mutant) and two tRNA-Arg
Components
  • tRNA pseudouridine(38/39) synthase
  • tRNA-Arg
KeywordsRNA 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
Pseudouridine synthase Pus3-like / Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA pseudouridine(38/39) synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLin, T.-Y. / Jezowski, J. / Glatt, S.
Funding support Poland, European Union, Switzerland, 3items
OrganizationGrant numberCountry
Polish National Science Centre2019/35/D/NZ1/02397 Poland
European Research Council (ERC)101001394European Union
Swiss National Science Foundation310030_184947 Switzerland
CitationJournal: Mol.Cell / Year: 2024
Title: The molecular basis of tRNA selectivity by human pseudouridine synthase 3 (PUS3)
Authors: Lin, T.-Y. / Jezowski, J. / Glatt, S.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine(38/39) synthase
B: tRNA pseudouridine(38/39) synthase
C: tRNA-Arg
D: tRNA-Arg


Theoretical massNumber of molelcules
Total (without water)160,3074
Polymers160,3074
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein tRNA pseudouridine(38/39) synthase / tRNA pseudouridine synthase 3 / tRNA pseudouridylate synthase 3 / tRNA-uridine isomerase 3


Mass: 55681.207 Da / Num. of mol.: 2 / Mutation: D118A
Source method: isolated from a genetically manipulated source
Details: D118A 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 tRNA-Arg


Mass: 24472.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Homodimer of human PUS3 and two tRNA-ArgCOMPLEXall0MULTIPLE SOURCES
2Pseudouridine synthase 3 (PUS3)COMPLEX#11RECOMBINANT
3tRNA-ArgCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8736

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.1particle selection
2EPUimage acquisition
4cryoSPARC4.1CTF correction
7UCSF ChimeraX1.6model fittingRigid body fit
9cryoSPARC4.1initial Euler assignment
10cryoSPARC4.1final Euler assignment
11cryoSPARC4.1classification
12cryoSPARC4.13D reconstruction
13PHENIX1.19.2-4158model refinementReal-space refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3192624
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74761 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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