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- EMDB-16917: Human apo pseudouridine synthase 3 (PUS3) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-16917
TitleHuman apo pseudouridine synthase 3 (PUS3)
Map datahuman full-legnth apo PUS3
Sample
  • Complex: homodimer of PUS3
    • Protein or peptide: pseudouridine syntase 3
KeywordsRNA 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
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
tRNA pseudouridine(38/39) synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLin T-Y / Glatt S / Koziej L
Funding support Poland, European Union, Switzerland, 3 items
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 apo pseudouridine synthase 3 (PUS3)
Authors: Lin T-Y / Glatt S
History
DepositionMar 27, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16917.png

Downloads & links

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Map

FileDownload / File: emd_16917.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman full-legnth apo PUS3
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.0573
Minimum - Maximum-0.058290984 - 0.17048551
Average (Standard dev.)0.00036348976 (±0.007825954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16917_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : homodimer of PUS3

EntireName: homodimer of PUS3
Components
  • Complex: homodimer of PUS3
    • Protein or peptide: pseudouridine syntase 3

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Supramolecule #1: homodimer of PUS3

SupramoleculeName: homodimer of PUS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550 KDa

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Macromolecule #1: pseudouridine syntase 3

MacromoleculeName: pseudouridine syntase 3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AMADNDTDRN QTEKLLKRVR ELEQEVQRLK KEQAKNKEDS NIRENSAGAG KTKRAFDFSA HGRRHVALRI AYMGWGYQGF ASQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR YTHILNRVLP ...String:
AMADNDTDRN QTEKLLKRVR ELEQEVQRLK KEQAKNKEDS NIRENSAGAG KTKRAFDFSA HGRRHVALRI AYMGWGYQGF ASQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR YTHILNRVLP PDIRILAWAP VEPSFSARFS CLERTYRYFF PRADLDIVTM DYAAQKYVGT HDFRNLCKMD VANGVINFQR TILSAQVQLV GQSPGEGRWQ EPFQLCQFEV TGQAFLYHQV RCMMAILFLI GQGMEKPEII DELLNIEKNP QKPQYSMAVE FPLVLYDCKF ENVKWIYDQE AQEFNITHLQ QLWANHAVKT HMLYSMLQGL DTVPVPCGIG PKMDGMTEWG NVKPSVIKQT SAFVEGVKMR TYKPLMDRPK CQGLESRIQH FVRRGRIEHP HLFHEEETKA KRDCNDTLEE ENTNLETPTK RVCVDTEIKS II

UniProtKB: tRNA pseudouridine(38/39) synthase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 8 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7353 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen 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

Particle selectionNumber selected: 334282
Startup modelType of model: INSILICO MODEL / In silico model: alphafold2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 63173
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 65000 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

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