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- EMDB-1129: Nucleotide-dependent bending flexibility of tubulin regulates mic... -

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Basic information

Entry
Database: EMDB / ID: EMD-1129
TitleNucleotide-dependent bending flexibility of tubulin regulates microtubule assembly.
Map dataThis is the reconstruction of the inner layer of the GDP-tubulin double-layered tube.
Sample
  • Sample: GDP-tubulin
  • Protein or peptide: tubulin
Biological speciesBos taurus (cattle)
Methodhelical reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsWang HW / Nogales E
CitationJournal: Nature / Year: 2005
Title: Nucleotide-dependent bending flexibility of tubulin regulates microtubule assembly.
Authors: Hong-Wei Wang / Eva Nogales /
Abstract: The atomic structure of tubulin in a polymerized, straight protofilament is clearly distinct from that in a curved conformation bound to a cellular depolymerizer. The nucleotide contents are ...The atomic structure of tubulin in a polymerized, straight protofilament is clearly distinct from that in a curved conformation bound to a cellular depolymerizer. The nucleotide contents are identical, and in both cases the conformation of the GTP-containing, intra-dimer interface is indistinguishable from the GDP-containing, inter-dimer contact. Here we present two structures corresponding to the start and end points in the microtubule polymerization and hydrolysis cycles that illustrate the consequences of nucleotide state on longitudinal and lateral assembly. In the absence of depolymerizers, GDP-bound tubulin shows distinctive intra-dimer and inter-dimer interactions and thus distinguishes the GTP and GDP interfaces. A cold-stable tubulin polymer with the non-hydrolysable GTP analogue GMPCPP, containing semi-conserved lateral interactions, supports a model in which the straightening of longitudinal interfaces happens sequentially, starting with a conformational change after GTP binding that straightens the dimer enough for the formation of lateral contacts into a non-tubular intermediate. Closure into a microtubule does not require GTP hydrolysis.
History
DepositionMay 11, 2005-
Header (metadata) releaseMay 12, 2005-
Map releaseMay 12, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1129.gif

Downloads & links

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Map

FileDownload / File: emd_1129.map.gz / Format: CCP4 / Size: 11 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the reconstruction of the inner layer of the GDP-tubulin double-layered tube.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4 Å/pix.
x 101 pix.
= 404. Å		4 Å/pix.
x 171 pix.
= 684. Å		4 Å/pix.
x 171 pix.
= 684. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 16.0 / Movie #1: 14
Minimum - Maximum-18.0 - 45.0
Average (Standard dev.)1.80313 (±5.77079)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-85-85-50
Dimensions171171101
Spacing171171101
CellA: 684 Å / B: 684 Å / C: 404 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z171171101
origin x/y/z0.0000.0000.000
length x/y/z684.000684.000404.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-85-85-50
NC/NR/NS171171101
D min/max/mean-18.00045.0001.803

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Supplemental data

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Sample components

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Entire : GDP-tubulin

EntireName: GDP-tubulin
Components
  • Sample: GDP-tubulin
  • Protein or peptide: tubulin

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Supramolecule #1000: GDP-tubulin

SupramoleculeName: GDP-tubulin / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: tubulin

MacromoleculeName: tubulin / type: protein_or_peptide / ID: 1 / Name.synonym: tubulin / Number of copies: 1 / Oligomeric state: dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: cattle / Tissue: brain / Organelle: cytoskeleton / Location in cell: cytosol
Molecular weightExperimental: 110 KDa / Theoretical: 110 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 6.8 / Details: 80 mM PIPES, 1 mM MgCl2, 1mM GDP, 30 mM MnCl2
GridDetails: 400 Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blot for 1.8 seconds before plunging with Vitrobot offset as -2 mm

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200K mag
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.7 µm / Number real images: 200 / Average electron dose: 15 e/Å2 / Bits/pixel: 14
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailshelices were formed from tubular crystals
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: MRC and home-made programs / Details: final maps were calculated from 19 tube images
CTF correctionDetails: each image

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