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- EMDB-15464: In situ subtomogram average of floating microtubule inner protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-15464
TitleIn situ subtomogram average of floating microtubule inner protein 13 (fMIP13)
Map dataIn situ subtomogram average of floating microtubule inner protein 13
Sample
  • Cell: fMIP13 obtained from human induced pluripotent stem cells derived neuron.
Keywordsmicrotubule-associated protein / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsChakraborty S / Mahamid J / Martinez-Sanchez A / Baumeister W
Funding support1 items
OrganizationGrant numberCountry
Other government
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-ET suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules.
Authors: Saikat Chakraborty / Antonio Martinez-Sanchez / Florian Beck / Mauricio Toro-Nahuelpan / In-Young Hwang / Kyung-Min Noh / Wolfgang Baumeister / Julia Mahamid /
Abstract: The functional architecture of the long-lived neuronal microtubule (MT) cytoskeleton is maintained by various MT-associated proteins (MAPs), most of which are known to bind to the MT outer surface. ...The functional architecture of the long-lived neuronal microtubule (MT) cytoskeleton is maintained by various MT-associated proteins (MAPs), most of which are known to bind to the MT outer surface. However, electron microscopy (EM) has long ago revealed the presence of particles inside the lumens of neuronal MTs, of yet unknown identity and function. Here, we use cryogenic electron tomography (cryo-ET) to analyze the three-dimensional (3D) organization and structures of MT lumenal particles in primary hippocampal neurons, human induced pluripotent stem cell-derived neurons, and pluripotent and differentiated P19 cells. We obtain in situ density maps of several lumenal particles from the respective cells and detect common structural features underscoring their potential overarching functions. Mass spectrometry-based proteomics combined with structural modeling suggest that a subset of lumenal particles could be tubulin-binding cofactors (TBCs) bound to tubulin monomers. A different subset of smaller particles, which remains unidentified, exhibits densities that bridge across the MT protofilaments. We show that increased lumenal particle concentration within MTs is concomitant with neuronal differentiation and correlates with higher MT curvatures. Enrichment of lumenal particles around MT lattice defects and at freshly polymerized MT open-ends suggests a MT protective role. Together with the identified structural resemblance of a subset of particles to TBCs, these results hint at a role in local tubulin proteostasis for the maintenance of long-lived neuronal MTs.
#1: Journal: Biorxiv / Year: 2024
Title: Cryo-electron tomography suggests tubulin chaperones form a subset of microtubule lumenal particles with a role in maintaining neuronal microtubules
Authors: Chakraborty S / Martinez-Sanchez A / Beck F / Toro-Nahuelpan M / Hwang IY / Noh KM / Baumeister W / Mahamid J
History
DepositionJul 25, 2022-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15464.png

Downloads & links

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Map

FileDownload / File: emd_15464.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ subtomogram average of floating microtubule inner protein 13
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 128 pix.
= 272.512 Å		2.13 Å/pix.
x 128 pix.
= 272.512 Å		2.13 Å/pix.
x 128 pix.
= 272.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.129 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2378386 - 0.2742295
Average (Standard dev.)-0.004679056 (±0.0254355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 272.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: In situ subtomogram average of floating microtubule inner protein 13

Fileemd_15464_half_map_1.map
AnnotationIn situ subtomogram average of floating microtubule inner protein 13
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ subtomogram average of floating microtubule inner protein 13

Fileemd_15464_half_map_2.map
AnnotationIn situ subtomogram average of floating microtubule inner protein 13
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : fMIP13 obtained from human induced pluripotent stem cells derived...

EntireName: fMIP13 obtained from human induced pluripotent stem cells derived neuron.
Components
  • Cell: fMIP13 obtained from human induced pluripotent stem cells derived neuron.

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Supramolecule #1: fMIP13 obtained from human induced pluripotent stem cells derived...

SupramoleculeName: fMIP13 obtained from human induced pluripotent stem cells derived neuron.
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 310 K / Instrument: LEICA EM GP
DetailsFrozen hydrated human induced pluripotent stem cells derived neurons.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 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: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000
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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number subtomograms used: 2151
ExtractionNumber tomograms: 8 / Number images used: 8635 / Software - Name: IMOD (ver. 4.9.0)
Final 3D classificationSoftware - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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