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- PDB-8okd: Human pseudouridine synthase 3 and tRNA-Gln -

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Basic information

Entry
Database: PDB / ID: 8okd
TitleHuman pseudouridine synthase 3 and tRNA-Gln
Components
  • human tRNA-Gln (70-MER)
  • tRNA pseudouridine(38/39) synthase
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: 3.1 Å
AuthorsLin, T.-Y. / 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: Human pseudouridine synthase 3 (PUS3) and tRNA-Gln
Authors: Lin, T.-Y. / Glatt, S.
History
DepositionMar 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA pseudouridine(38/39) synthase
B: tRNA pseudouridine(38/39) synthase
C: human tRNA-Gln (70-MER)
X: human tRNA-Gln (70-MER)


Theoretical massNumber of molelcules
Total (without water)159,5034
Polymers159,5034
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10280 Å2
ΔGint-91 kcal/mol
Surface area49000 Å2

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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: 55704.199 Da / Num. of mol.: 2 / Mutation: D118A
Source method: isolated from a genetically manipulated source
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 human tRNA-Gln (70-MER)


Mass: 24047.236 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 PUS3 and tRNA-Gln complexCOMPLEXall0MULTIPLE SOURCES
2Pseudouridine synthase 3 (PUS3)COMPLEX#11RECOMBINANT
3tRNA-GlnCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.11 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 supportDetails: 8 mA / Grid material: COPPER / Grid type: Quantifoil
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 defocus max: 1800 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: 8320

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
2EPUimage acquisition
4cryoSPARC4.1CTF correction
9cryoSPARC4.1initial Euler assignment
10cryoSPARC4.1final Euler assignment
11cryoSPARC4.1classification
12cryoSPARC4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 482246
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147307 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038212
ELECTRON MICROSCOPYf_angle_d0.49411778
ELECTRON MICROSCOPYf_dihedral_angle_d12.9442312
ELECTRON MICROSCOPYf_chiral_restr0.0341406
ELECTRON MICROSCOPYf_plane_restr0.0031002

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