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- EMDB-16436: microtubule decorated with tubulin oligomers in presence of APC C... -

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Basic information

Entry
Database: EMDB / ID: EMD-16436
Titlemicrotubule decorated with tubulin oligomers in presence of APC C-terminal domain. (here only map corresponding to the external tubulin oligomer is represented)
Map data
Sample
  • Complex: ring-like tubulin oligomers decorating microtubules.
    • Protein or peptide: ALPHA-TUBULIN
    • Protein or peptide: BETA-TUBULIN
Biological speciesBos taurus (domestic cattle)
Methodhelical reconstruction / cryo EM / Resolution: 36.9 Å
AuthorsSerre L / Arnal I
Funding support France, 1 items
OrganizationGrant numberCountry
ATIP-Avenir France
CitationJournal: J.Cell.Sci. / Year: 2022
Title: The mitotic role of Adenomatous Polyposis Coli requires its bilateral interaction with tubulin and microtubules
Authors: Serre L / Delaroche J / Vinit A / Schoehn G / Denarier E / Fourest-Lieuvin A / Arnal I
History
DepositionJan 6, 2023-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16436.png

Downloads & links

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Map

FileDownload / File: emd_16436.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 320 pix.
= 627.2 Å		1.96 Å/pix.
x 320 pix.
= 627.2 Å		1.96 Å/pix.
x 320 pix.
= 627.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0014
Minimum - Maximum-0.004146451 - 0.018413927
Average (Standard dev.)0.00014728677 (±0.0009212207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 627.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_16436_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_16436_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 : ring-like tubulin oligomers decorating microtubules.

EntireName: ring-like tubulin oligomers decorating microtubules.
Components
  • Complex: ring-like tubulin oligomers decorating microtubules.
    • Protein or peptide: ALPHA-TUBULIN
    • Protein or peptide: BETA-TUBULIN

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Supramolecule #1: ring-like tubulin oligomers decorating microtubules.

SupramoleculeName: ring-like tubulin oligomers decorating microtubules. / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: brain

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Macromolecule #1: ALPHA-TUBULIN

MacromoleculeName: ALPHA-TUBULIN / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: brain
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH S FGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH S FGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IY DICRRNL DIERPTYTNL NRLIGQIVSS ITASLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEK AYHEQL SVAEITNACF EPANQMVKCD PRHGKYMACC LLYRGDVVPK DVNAAIATIK TKRTIQFVDW CPTG FKVGI NYQPPTVVPG GDLAKVQRAV CMLSNTTAIA EAWARLDHKF DLMYAKRAFV HWYVGEGMEE GEFSE ARED MAALEKDYEE VGVDSVEGEG EEEGEEY

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Macromolecule #2: BETA-TUBULIN

MacromoleculeName: BETA-TUBULIN / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Brain
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKESESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VMPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQMFDS KNMM AACDP RHGRYLTVAA IFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMS ATFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQDATADEQ GEGHEDEEKD EGG

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.7 / Details: 80 mM Pipes, 1 mM MgCl2, 1mM EGTA, 50 mM KCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.61 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.676 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 36.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: resolution estimated from masked FSC (0.143) is 25 A.
Number images used: 5928
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6b0c


Details: tubulin dimers extracted from the external tubulin ring was used to generate a reference map
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
FSC plot (resolution estimation)

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