[English] 日本語
Yorodumi
- EMDB-19833: Human pseudouridine synthase 3 (PUS3 D118A mutant) and two pre-tR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19833
TitleHuman pseudouridine synthase 3 (PUS3 D118A mutant) and two pre-tRNA-Arg
Map data
Sample
  • Complex: Homodimer of human PUS3 and two pre-tRNA-Arg
    • Complex: Pseudouridine synthase 3 (PUS3)
      • Protein or peptide: tRNA pseudouridine(38/39) synthase
    • Complex: tRNA-Arg
      • RNA: pre-tRNA-Arg
KeywordsRNA modification / pseudouridylation / tRNA / homodimer / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA pseudouridine38/39 synthase / tRNA pseudouridine(38/39) synthase activity / mRNA pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification in the nucleus and cytosol / tRNA modification / RNA binding / nucleus / cytosol / cytoplasm
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: 2.97 Å
AuthorsLin T-Y / Jezowski J / Glatt S
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: The molecular basis of tRNA selectivity by human pseudouridine synthase 3.
Authors: Ting-Yu Lin / Leon Kleemann / Jakub Jeżowski / Dominika Dobosz / Michał Rawski / Paulina Indyka / Grzegorz Ważny / Rahul Mehta / Andrzej Chramiec-Głąbik / Łukasz Koziej / Tristan Ranff ...Authors: Ting-Yu Lin / Leon Kleemann / Jakub Jeżowski / Dominika Dobosz / Michał Rawski / Paulina Indyka / Grzegorz Ważny / Rahul Mehta / Andrzej Chramiec-Głąbik / Łukasz Koziej / Tristan Ranff / Christian Fufezan / Mateusz Wawro / Jakub Kochan / Joanna Bereta / Sebastian A Leidel / Sebastian Glatt /
Abstract: Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. ...Pseudouridine (Ψ), the isomer of uridine, is ubiquitously found in RNA, including tRNA, rRNA, and mRNA. Human pseudouridine synthase 3 (PUS3) catalyzes pseudouridylation of position 38/39 in tRNAs. However, the molecular mechanisms by which it recognizes its RNA targets and achieves site specificity remain elusive. Here, we determine single-particle cryo-EM structures of PUS3 in its apo form and bound to three tRNAs, showing how the symmetric PUS3 homodimer recognizes tRNAs and positions the target uridine next to its active site. Structure-guided and patient-derived mutations validate our structural findings in complementary biochemical assays. Furthermore, we deleted PUS1 and PUS3 in HEK293 cells and mapped transcriptome-wide Ψ sites by Pseudo-seq. Although PUS1-dependent sites were detectable in tRNA and mRNA, we found no evidence that human PUS3 modifies mRNAs. Our work provides the molecular basis for PUS3-mediated tRNA modification in humans and explains how its tRNA modification activity is linked to intellectual disabilities.
History
DepositionMar 12, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19833.png

Downloads & links

-
Map

FileDownload / File: emd_19833.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.18064523 - 0.4121738
Average (Standard dev.)0.0030787971 (±0.014664318)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_19833_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19833_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homodimer of human PUS3 and two pre-tRNA-Arg

EntireName: Homodimer of human PUS3 and two pre-tRNA-Arg
Components
  • Complex: Homodimer of human PUS3 and two pre-tRNA-Arg
    • Complex: Pseudouridine synthase 3 (PUS3)
      • Protein or peptide: tRNA pseudouridine(38/39) synthase
    • Complex: tRNA-Arg
      • RNA: pre-tRNA-Arg

-
Supramolecule #1: Homodimer of human PUS3 and two pre-tRNA-Arg

SupramoleculeName: Homodimer of human PUS3 and two pre-tRNA-Arg / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 180 KDa

-
Supramolecule #2: Pseudouridine synthase 3 (PUS3)

SupramoleculeName: Pseudouridine synthase 3 (PUS3) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: tRNA-Arg

SupramoleculeName: tRNA-Arg / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: tRNA pseudouridine(38/39) synthase

MacromoleculeName: tRNA pseudouridine(38/39) synthase / type: protein_or_peptide / ID: 1 / Details: D118A single mutation / Number of copies: 2 / Enantiomer: LEVO / EC number: tRNA pseudouridine38/39 synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.681207 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL ...String:
MAYNDTDRNQ TEKLLKRVRE LEQEVQRLKK EQAKNKEDSN IRENSAGAGK TKRAFDFSAH GRRHVALRIA YMGWGYQGFA SQENTNNTI EEKLFEALTK TRLVESRQTS NYHRCGRTAK GVSAFGQVIS LDLRSQFPRG RDSEDFNVKE EANAAAEEIR Y THILNRVL PPDIRILAWA PVEPSFSARF SCLERTYRYF FPRADLDIVT MDYAAQKYVG THDFRNLCKM DVANGVINFQ RT ILSAQVQ LVGQSPGEGR WQEPFQLCQF EVTGQAFLYH QVRCMMAILF LIGQGMEKPE IIDELLNIEK NPQKPQYSMA VEF PLVLYD CKFENVKWIY DQEAQEFNIT HLQQLWANHA VKTHMLYSML QGLDTVPVPC GIGPKMDGMT EWGNVKPSVI KQTS AFVEG VKMRTYKPLM DRPKCQGLES RIQHFVRRGR IEHPHLFHEE ETKAKRDCND TLEEENTNLE TPTKRVCVDT EIKSI I

UniProtKB: tRNA pseudouridine(38/39) synthase

-
Macromolecule #2: pre-tRNA-Arg

MacromoleculeName: pre-tRNA-Arg / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.2989 KDa
SequenceString:
GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAGCU GAGCCUAGUG UGGUCAUUCA AAGGUUGUGG GUUCGAGUCC CACCAGAGU CGCCA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8673 / 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: 1.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 9139918
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 381809
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 185580 / Software - Name: cryoSPARC (ver. 4.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more