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- EMDB-4188: Cryo-EM structure of microtubule co-polymerized with SSNA1. -

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Basic information

Entry
Database: EMDB / ID: EMD-4188
TitleCryo-EM structure of microtubule co-polymerized with SSNA1.
Map data
Sample
  • Complex: SSNA1 in complex with porcine microtubules
Biological speciesChlamydo
Methodhelical reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsBasnet N / Mizuno N
CitationJournal: Nat Cell Biol / Year: 2018
Title: Direct induction of microtubule branching by microtubule nucleation factor SSNA1.
Authors: Nirakar Basnet / Hana Nedozralova / Alvaro H Crevenna / Satish Bodakuntla / Thomas Schlichthaerle / Michael Taschner / Giovanni Cardone / Carsten Janke / Ralf Jungmann / Maria M Magiera / ...Authors: Nirakar Basnet / Hana Nedozralova / Alvaro H Crevenna / Satish Bodakuntla / Thomas Schlichthaerle / Michael Taschner / Giovanni Cardone / Carsten Janke / Ralf Jungmann / Maria M Magiera / Christian Biertümpfel / Naoko Mizuno /
Abstract: Microtubules are central elements of the eukaryotic cytoskeleton that often function as part of branched networks. Current models for branching include nucleation of new microtubules from severed ...Microtubules are central elements of the eukaryotic cytoskeleton that often function as part of branched networks. Current models for branching include nucleation of new microtubules from severed microtubule seeds or from γ-tubulin recruited to the side of a pre-existing microtubule. Here, we found that microtubules can be directly remodelled into branched structures by the microtubule-remodelling factor SSNA1 (also known as NA14 or DIP13). The branching activity of SSNA1 relies on its ability to self-assemble into fibrils in a head-to-tail fashion. SSNA1 fibrils guide protofilaments of a microtubule to split apart to form daughter microtubules. We further found that SSNA1 localizes at axon branching sites and has a key role in neuronal development. SSNA1 mutants that abolish microtubule branching in vitro also fail to promote axon development and branching when overexpressed in neurons. We have, therefore, discovered a mechanism for microtubule branching and implicated its role in neuronal development.
History
DepositionNov 30, 2017-
Header (metadata) releaseJan 17, 2018-
Map releaseDec 12, 2018-
UpdateDec 12, 2018-
Current statusDec 12, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4188.png

Downloads & links

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Map

FileDownload / File: emd_4188.map.gz / Format: CCP4 / Size: 23 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.003 / Movie #1: 0.003
Minimum - Maximum-0.019603234 - 0.029958658
Average (Standard dev.)0.000003971154 (±0.0024539824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-122
Dimensions224224120
Spacing224224120
CellA: 300.16 Å / B: 300.16 Å / C: 160.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z224224120
origin x/y/z0.0000.0000.000
length x/y/z300.160300.160160.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-153-266-98
NX/NY/NZ528514389
MAP C/R/S123
start NC/NR/NS00-122
NC/NR/NS224224120
D min/max/mean-0.0200.0300.000

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Supplemental data

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Sample components

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Entire : SSNA1 in complex with porcine microtubules

EntireName: SSNA1 in complex with porcine microtubules
Components
  • Complex: SSNA1 in complex with porcine microtubules

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Supramolecule #1: SSNA1 in complex with porcine microtubules

SupramoleculeName: SSNA1 in complex with porcine microtubules / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydo

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 6.8 / Details: 80mM PIPES, 1 mM EGTA, 1 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.08 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.37308 Å
Applied symmetry - Helical parameters - Δ&Phi: 27.692 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30625
Final angle assignmentType: NOT APPLICABLE

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