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- EMDB-77046: Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) i... -

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Basic information

Entry
Database: EMDB / ID: EMD-77046
TitleThermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Escherichia coli tRNA(THR)
Map dataLocal refinement with a focused mask on TsaB2D-tRNA
Sample
  • Complex: Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)
    • RNA: tRNA(THR)
    • Protein or peptide: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
    • Protein or peptide: tRNA N6-adenosine threonylcarbamoyltransferase
  • Ligand: MAGNESIUM ION
KeywordsTsaB2D2 / threonylcarbamoyl transfer complex / tRNA / t6A / N6-threonylcarbamoyl adenosine / t6A37 / transfer-RNA / BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN-RNA complex / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / tRNA N(6)-L-threonylcarbamoyladenine synthase activity / tRNA threonylcarbamoyladenosine modification / iron ion binding / cytoplasm / cytosol
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase, TsaD / tRNA threonylcarbamoyl adenosine modification protein TsaB / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKutchuashvili A / Swairjo MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110588 United States
CitationJournal: To Be Published
Title: Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Escherichia coli tRNA(THR)
Authors: Kutchuashvili A / Swairjo MA
History
DepositionMay 4, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77046.png

Downloads & links

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Map

FileDownload / File: emd_77046.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement with a focused mask on TsaB2D-tRNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.576 Å		0.83 Å/pix.
x 360 pix.
= 297.576 Å		0.83 Å/pix.
x 360 pix.
= 297.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8266 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.15881202 - 0.4318902
Average (Standard dev.)0.00031022256 (±0.0068491385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.57602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_77046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map

Fileemd_77046_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77046_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77046_half_map_2.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 : Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)

EntireName: Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)
Components
  • Complex: Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)
    • RNA: tRNA(THR)
    • Protein or peptide: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
    • Protein or peptide: tRNA N6-adenosine threonylcarbamoyltransferase
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)

SupramoleculeName: Thermotoga maritima TsaB2D2 in complex with Escherichia coli tRNA(THR)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 146 kDa/nm

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Macromolecule #1: tRNA(THR)

MacromoleculeName: tRNA(THR) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.585605 KDa
SequenceString:
GCCGAUAUAG CUCAGUUGGU AGAGCAGCGC AUUCGU(T6A)AUG CGAAGGUCGU AGGUUCGACU CCUAUUAUCG GCACCA

GENBANK: GENBANK: CP053606.1

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Macromolecule #2: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

MacromoleculeName: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 23.461275 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSHMASNVLA LDTSQRIRIG LRKGEDLFEI SYTGEKKHAE ILPVVVKKLL DELDLKVKDL DVVGVGIGPG GLTGLRVGIA TVVGLVSPY DIPVAPLNSF EMTAKSCPAD GVVLVARRAR KGYHYCAVYL KDKGLNPLKE PSVVSDEELE EITKEFSPKI V LKDDLLIS ...String:
GSHMASNVLA LDTSQRIRIG LRKGEDLFEI SYTGEKKHAE ILPVVVKKLL DELDLKVKDL DVVGVGIGPG GLTGLRVGIA TVVGLVSPY DIPVAPLNSF EMTAKSCPAD GVVLVARRAR KGYHYCAVYL KDKGLNPLKE PSVVSDEELE EITKEFSPKI V LKDDLLIS PAVLVEESER LFREKKTIHY YEIEPLYLQK SIAELNWEKK KRG

UniProtKB: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

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Macromolecule #3: tRNA N6-adenosine threonylcarbamoyltransferase

MacromoleculeName: tRNA N6-adenosine threonylcarbamoyltransferase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: N6-L-threonylcarbamoyladenine synthase
Source (natural)Organism: Thermotoga maritima (bacteria)
Molecular weightTheoretical: 38.661316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHVG TGSNDDDDKS PDPIEGRMRV LGIETSCDET AVAVLDDGKN VVVNFTVSQI EVHQKFGGVV PEVAARHHLK NLPILLKKA FEKVPPETVD VVAATYGPGL IGALLVGLSA AKGLAISLEK PFVGVNHVEA HVQAVFLANP DLKPPLVVLM V SGGHTQLM ...String:
MAHHHHHHVG TGSNDDDDKS PDPIEGRMRV LGIETSCDET AVAVLDDGKN VVVNFTVSQI EVHQKFGGVV PEVAARHHLK NLPILLKKA FEKVPPETVD VVAATYGPGL IGALLVGLSA AKGLAISLEK PFVGVNHVEA HVQAVFLANP DLKPPLVVLM V SGGHTQLM KVDEDYSMEV LGETLDDSAG EAFDKVARLL GLGYPGGPVI DRVAKKGDPE KYSFPRPMLD DDSYNFSFAG LK TSVLYFL QREKGYKVED VAASFQKAVV DILVEKTFRL ARNLGIRKIA FVGGVAANSM LREEVRKRAE RWNYEVFFPP LEL CTDNAL MVAKAGYEKA KRGMFSPLSL NADPNLNV

UniProtKB: tRNA N6-adenosine threonylcarbamoyltransferase

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
50.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
1.0 mMC4H10O2S2dithiothreitol
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 294 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6n9a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 323313
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 300000

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Atomic model buiding 1

RefinementOverall B value: 141
Output model

PDB-13fn:
Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Escherichia coli tRNA(THR)

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