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- PDB-9hjc: Cryo-EM structure of thiamine-bound human TPK1 -

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Basic information

Entry
Database: PDB / ID: 9hjc
TitleCryo-EM structure of thiamine-bound human TPK1
ComponentsThiamine pyrophosphokinase 1
KeywordsTRANSFERASE / Thiamine / Kinase / Thiamine metabolism dysfunction syndrome 5
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Diphosphotransferases / UTP thiamine diphosphokinase activity / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / Vitamin B1 (thiamin) metabolism / regulation of pyruvate decarboxylation to acetyl-CoA / thiamine diphosphate biosynthetic process / kinase activity / ATP binding ...Transferases; Transferring phosphorus-containing groups; Diphosphotransferases / UTP thiamine diphosphokinase activity / thiamine diphosphokinase activity / thiamine binding / thiamine metabolic process / Vitamin B1 (thiamin) metabolism / regulation of pyruvate decarboxylation to acetyl-CoA / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / identical protein binding / cytosol
Similarity search - Function
Thiamin pyrophosphokinase, eukaryotic / Thiamin pyrophosphokinase, thiamin-binding domain superfamily / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase, thiamin-binding domain / Thiamin pyrophosphokinase, vitamin B1 binding domain / Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily
Similarity search - Domain/homology
Chem-VIB / Thiamine pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsGabriel, F. / Loew, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Thesis / Year: 2024
Title: Structural Basis of Membrane Transport and Pyrophosphorylation of Thiamine in Humans
Authors: Gabriel, F.
#1: Journal: To Be Published
Title: Cryo-EM structure of the human TPK1
Authors: Gabriel, F. / Loew, C.
History
DepositionNov 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiamine pyrophosphokinase 1
B: Thiamine pyrophosphokinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7626
Polymers62,1832
Non-polymers5794
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 Thiamine pyrophosphokinase 1 / hTPK1 / Placental protein 20 / PP20 / Thiamin pyrophosphokinase 1


Mass: 31091.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPK1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3S4
#2: Chemical ChemComp-VIB / 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / THIAMIN / VITAMIN B1


Mass: 265.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Thiamine-bound TPK1 homodimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 32 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
120 mMTris-HCl1
2150 mMNaCl1
30.002 %LMNG1
40.0002 %CHS1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 283 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 defocus max: 1700 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3711795 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023961
ELECTRON MICROSCOPYf_angle_d0.4595387
ELECTRON MICROSCOPYf_dihedral_angle_d7.512523
ELECTRON MICROSCOPYf_chiral_restr0.042616
ELECTRON MICROSCOPYf_plane_restr0.003685

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