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- PDB-13fo: Thermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) i... -

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Basic information

Entry
Database: PDB / ID: 13fo
TitleThermotoga maritima threonylcarbamoyl transfer complex (TsaB2D) in complex with Thermotoga maritima tRNA(LYS)
Components
  • T. maritima tRNA(LYS)
  • tRNA N6-adenosine threonylcarbamoyltransferase
  • tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
KeywordsRNA BINDING PROTEIN/RNA / TsaB2D2 / 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
: / RNA / RNA (> 10) / tRNA N6-adenosine threonylcarbamoyltransferase / tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKutchuashvili, A. / Swairjo, M.A.
Funding support United States, 1items
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 Thermotoga maritima tRNA(LYS)
Authors: Kutchuashvili, A. / Swairjo, M.A.
History
DepositionMay 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
D: tRNA N6-adenosine threonylcarbamoyltransferase
T: T. maritima tRNA(LYS)
X: tRNA threonylcarbamoyladenosine biosynthesis protein TsaB


Theoretical massNumber of molelcules
Total (without water)110,0534
Polymers110,0534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein tRNA threonylcarbamoyladenosine biosynthesis protein TsaB / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB


Mass: 23461.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tsaB, TM_0874, Tmari_0876 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZX7
#2: Protein tRNA N6-adenosine threonylcarbamoyltransferase / N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine ...N6-L-threonylcarbamoyladenine synthase / t(6)A synthase / t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD / tRNA threonylcarbamoyladenosine biosynthesis protein TsaD


Mass: 38661.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tsaD, gcp, TM_0145 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WXZ2, N6-L-threonylcarbamoyladenine synthase
#3: RNA chain T. maritima tRNA(LYS)


Mass: 24469.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermotoga maritima (bacteria) / References: GenBank: 811629352
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermotoga maritima TsaB2D2 in complex with Thermotoga maritima tRNA(LYS)
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 146 kDa/nm / Experimental value: YES
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
250 mMpotassium chlorideKCl1
35 mMmagnesium chlorideMgCl21
41 mMdithiothreitolC4H10O2S21
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Thermotoga maritima TsaB2D2 in complex with Thermotoga maritima tRNA(LYS)
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Au-flat 1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 294 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM4.1.2image acquisition
4cryoSPARCCTF correction
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63799 / Symmetry type: POINT
Atomic model buildingB value: 124
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047458
ELECTRON MICROSCOPYf_angle_d0.61810454
ELECTRON MICROSCOPYf_dihedral_angle_d19.4251867
ELECTRON MICROSCOPYf_chiral_restr0.041266
ELECTRON MICROSCOPYf_plane_restr0.0051063

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