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- PDB-9j4d: Cryo-EM structure of P25alpha core fibril -

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Basic information

Entry
Database: PDB / ID: 9j4d
TitleCryo-EM structure of P25alpha core fibril
ComponentsTubulin polymerization-promoting protein
KeywordsCYTOSOLIC PROTEIN / PROTEIN FIBRIL / amyloid
Function / homology
Function and homology information


microtubule nucleation by microtubule organizing center / postsynaptic Golgi apparatus / myelin assembly / astral microtubule organization / positive regulation of myelination / microtubule bundle formation / oligodendrocyte development / positive regulation of protein polymerization / negative regulation of tubulin deacetylation / microtubule polymerization ...microtubule nucleation by microtubule organizing center / postsynaptic Golgi apparatus / myelin assembly / astral microtubule organization / positive regulation of myelination / microtubule bundle formation / oligodendrocyte development / positive regulation of protein polymerization / negative regulation of tubulin deacetylation / microtubule polymerization / microtubule organizing center / oligodendrocyte differentiation / tubulin binding / regulation of microtubule cytoskeleton organization / positive regulation of protein-containing complex assembly / mitotic spindle / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cell division / GTPase activity / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
P25-alpha / p25-alpha / EF-hand domain pair
Similarity search - Domain/homology
Tubulin polymerization-promoting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsXia, W.C. / Sun, Y.P. / Huang, C.A. / Liu, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of P25alpha core fibril
Authors: Xia, W.C. / Sun, Y.P. / Huang, C.A. / Liu, C.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Tubulin polymerization-promoting protein
C: Tubulin polymerization-promoting protein
D: Tubulin polymerization-promoting protein
E: Tubulin polymerization-promoting protein
A: Tubulin polymerization-promoting protein
B: Tubulin polymerization-promoting protein


Theoretical massNumber of molelcules
Total (without water)87,5806
Polymers87,5806
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
Tubulin polymerization-promoting protein / TPPP / 25 kDa brain-specific protein / TPPP/p25 / p24 / p25-alpha


Mass: 14596.640 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPPP, TPPP1 / Production host: Escherichia coli (E. coli)
References: UniProt: O94811, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of P25alpha core fibril / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 178.46 ° / Axial rise/subunit: 2.39 Å / Axial symmetry: C1
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139740 / Symmetry type: HELICAL

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