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- EMDB-52212: Cryo-EM structure of thiamine-bound human TPK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-52212
TitleCryo-EM structure of thiamine-bound human TPK1
Map data
Sample
  • Complex: Thiamine-bound TPK1 homodimer
    • Protein or peptide: Thiamine pyrophosphokinase 1
  • Ligand: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
  • Ligand: MAGNESIUM ION
KeywordsThiamine / Kinase / Thiamine metabolism dysfunction syndrome 5 / TRANSFERASE
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
Thiamine pyrophosphokinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsGabriel F / Loew C
Funding support1 items
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, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52212.png

Downloads & links

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Map

FileDownload / File: emd_52212.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 384 pix.
= 224.224 Å		0.58 Å/pix.
x 384 pix.
= 224.224 Å		0.58 Å/pix.
x 384 pix.
= 224.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58392 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-8.474351 - 11.777547999999999
Average (Standard dev.)-0.002538921 (±0.22163823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 224.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52212_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52212_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 : Thiamine-bound TPK1 homodimer

EntireName: Thiamine-bound TPK1 homodimer
Components
  • Complex: Thiamine-bound TPK1 homodimer
    • Protein or peptide: Thiamine pyrophosphokinase 1
  • Ligand: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Thiamine-bound TPK1 homodimer

SupramoleculeName: Thiamine-bound TPK1 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32 kDa/nm

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Macromolecule #1: Thiamine pyrophosphokinase 1

MacromoleculeName: Thiamine pyrophosphokinase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.091348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEHAFTPLEP LLSTGNLKYC LVILNQPLDN YFRHLWNKAL LRACADGGAN RLYDITEGER ESFLPEFING DFDSIRPEVR EYYATKGCE LISTPDQDHT DFTKCLKMLQ KKIEEKDLKV DVIVTLGGLA GRFDQIMASV NTLFQATHIT PFPIIIIQEE S LIYLLQPG ...String:
MEHAFTPLEP LLSTGNLKYC LVILNQPLDN YFRHLWNKAL LRACADGGAN RLYDITEGER ESFLPEFING DFDSIRPEVR EYYATKGCE LISTPDQDHT DFTKCLKMLQ KKIEEKDLKV DVIVTLGGLA GRFDQIMASV NTLFQATHIT PFPIIIIQEE S LIYLLQPG KHRLHVDTGM EGDWCGLIPV GQPCMQVTTT GLKWNLTNDV LAFGTLVSTS NTYDGSGVVT VETDHPLLWT MA IKSLEVL FQGPAGRAGE QKLISEEDLN SAVDHHHHHH

UniProtKB: Thiamine pyrophosphokinase 1

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Macromolecule #2: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-M...

MacromoleculeName: 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM
type: ligand / ID: 2 / Number of copies: 2 / Formula: VIB
Molecular weightTheoretical: 265.355 Da
Chemical component information

ChemComp-VIB:
3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM / medication*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
20.0 mMTris-HCl
150.0 mMNaCl
0.002 %LMNG
0.0002 %CHS
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3711795
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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