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- EMDB-15690: Cryo-EM structure of the Tb ADAT2/3 deaminase in complex with tRNA -

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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, putative
    • Protein or peptide: Deaminase, putative
  • Ligand: ZINC ION
KeywordsADAT / inosine / tRNA modification / deaminase / cryo-EM structure / Trypanosoma brucei / RNA BINDING PROTEIN
Function / homology
Function and homology information


tRNA(adenine34) deaminase / 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 / tRNA-specific adenosine deaminase activity / hydrolase activity / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
tRNA-specific adenosine deaminase / MafB19-like deaminase / 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
tRNA(adenine(34)) deaminase / 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15690.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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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)

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Sample components

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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, putative
    • Protein or peptide: Deaminase, putative
  • Ligand: ZINC ION

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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

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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

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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

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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: tRNA(adenine(34)) deaminase

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Macromolecule #4: ZINC ION

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

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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

Concentration0.07 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

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Electron microscopy

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

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Image processing

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

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