[English] 日本語
Yorodumi
- EMDB-15690: Cryo-EM structure of the Tb ADAT2/3 deaminase in complex with tRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15690
TitleCryo-EM structure of the Tb ADAT2/3 deaminase in complex with tRNA
Map dataFinal non b factor sharpened cryosparc map
Sample
  • Complex: ADAT2/3 in complex with tRNA
    • RNA: RNA (75-MER)
    • Protein or peptide: Deaminase, putativeDeamination
    • Protein or peptide: Deaminase, putativeDeamination
  • Ligand: ZINC ION
KeywordsADAT / inosine / tRNA modification / deaminase / cryo-EM structure / Trypanosoma brucei / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / hydrolase activity / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like
Similarity search - Domain/homology
Deaminase, putative / Deaminase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote) / Trypanosoma brucei (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDolce LG / Tengo L / Weis F / Kowalinski E
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0016 France
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3.
Authors: Luciano G Dolce / Aubree A Zimmer / Laura Tengo / Félix Weis / Mary Anne T Rubio / Juan D Alfonzo / Eva Kowalinski /
Abstract: The essential deamination of adenosine A to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three ...The essential deamination of adenosine A to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.
History
DepositionAug 29, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15690.png

Downloads & links

-
Map

FileDownload / File: emd_15690.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal non b factor sharpened cryosparc map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.117478535 - 0.37571403
Average (Standard dev.)0.00023794259 (±0.011007088)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: deepEMhancer post processed map

Fileemd_15690_additional_1.map
AnnotationdeepEMhancer post processed map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_15690_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_15690_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ADAT2/3 in complex with tRNA

EntireName: ADAT2/3 in complex with tRNA
Components
  • Complex: ADAT2/3 in complex with tRNA
    • RNA: RNA (75-MER)
    • Protein or peptide: Deaminase, putativeDeamination
    • Protein or peptide: Deaminase, putativeDeamination
  • Ligand: ZINC ION

-
Supramolecule #1: ADAT2/3 in complex with tRNA

SupramoleculeName: ADAT2/3 in complex with tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote)
Molecular weightTheoretical: 90 KDa

-
Macromolecule #1: RNA (75-MER)

MacromoleculeName: RNA (75-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Trypanosoma brucei (eukaryote)
Molecular weightTheoretical: 24.132311 KDa
SequenceString:
GGCCGCUUAG CACAGUGGCA GUGCACCACU CUCGUAAAGU GGGGGUCGCG AGUUCGAUUC UCGCAGUGGC CUCCA

GENBANK: GENBANK: AC091702.3

-
Macromolecule #2: Deaminase, putative

MacromoleculeName: Deaminase, putative / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 23.547535 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVQDTGKDTN LKGTAEANES VVYCDVFMQA ALKEATCALE EGEVPVGCVL VKADSSTAAQ AQAGDDLALQ KLIVARGRNA TNRKGHGLA HAEFVAVEEL LRQATAGTSE NIGGGGNSGA VSQDLADYVL YVVVEPCIMC AAMLLYNRVR KVYFGCTNPR F GGNGTVLS ...String:
MVQDTGKDTN LKGTAEANES VVYCDVFMQA ALKEATCALE EGEVPVGCVL VKADSSTAAQ AQAGDDLALQ KLIVARGRNA TNRKGHGLA HAEFVAVEEL LRQATAGTSE NIGGGGNSGA VSQDLADYVL YVVVEPCIMC AAMLLYNRVR KVYFGCTNPR F GGNGTVLS VHNSYKGCSG EDAALIGYES CGGYRAEEAV VLLQQFYRRE NTNAPLGKRK RKD

UniProtKB: Deaminase, putative

-
Macromolecule #3: Deaminase, putative

MacromoleculeName: Deaminase, putative / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
Molecular weightTheoretical: 40.600254 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMEEVVV PEEPPKLVSA LATYVQQERL CTMFLSIANK LLPLKPHACH LKRIRRSSAT RVATAPMDGF AGGVICDKRD SSVATSTIS DGCERNSAAL GTPAAEKSHV LELLLSVGGP VDSSALKELE SAADTTVAVH RVWVPDRAPR SSAEEWTKWC Q IWPFATPK ...String:
GPDSMEEVVV PEEPPKLVSA LATYVQQERL CTMFLSIANK LLPLKPHACH LKRIRRSSAT RVATAPMDGF AGGVICDKRD SSVATSTIS DGCERNSAAL GTPAAEKSHV LELLLSVGGP VDSSALKELE SAADTTVAVH RVWVPDRAPR SSAEEWTKWC Q IWPFATPK PRVPTQLSEC EVGSIQRIFR TVVMPLAKRL RTDETLGIAA VLVDPSDGYR VLVSSGEEHA LKRGNSAACL GY VSNSGCR KSNRVVLDHP VTFVLKEVTR KQCKDREVEG DASYLANGMD MFVSHEPCVM CSMALVHSRV RRVFYCFPNP VHG GLGSTV SIHAIQELNH HFRVFRCDSR WLSDPEGVSS DHDNPYWEDL TVP

UniProtKB: Deaminase, putative

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.07 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 55.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105718
FSC plot (resolution estimation)

+
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