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- EMDB-5196: Structural map of MT 16-4 -

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Basic information

Entry
Database: EMDB / ID: EMD-5196
TitleStructural map of MT 16-4
Map dataStructural map of MT 16-4
Sample
  • Sample: The microtubule containing 16 protofilaments
  • Protein or peptide: microtubule with 16 protofilaments
Keywordsmicrotubule / ultrastructure / Cryoelectron Microscopy Computer-Assisted Image Processing
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsSui H / Downing KH
CitationJournal: Structure / Year: 2010
Title: Structural basis of interprotofilament interaction and lateral deformation of microtubules.
Authors: Haixin Sui / Kenneth H Downing /
Abstract: The diverse functions of microtubules require stiff structures possessing sufficient lateral flexibility to enable bending with high curvature. We used cryo-electron microscopy to investigate the ...The diverse functions of microtubules require stiff structures possessing sufficient lateral flexibility to enable bending with high curvature. We used cryo-electron microscopy to investigate the molecular basis for these critical mechanical properties. High-quality structural maps were used to build pseudoatomic models of microtubules containing 11-16 protofilaments, representing a wide range of lateral curvature. Protofilaments in all these microtubules were connected primarily via interprotofilament interactions between the M loops, and the H1'-S2 and H2-S3 loops. We postulate that the tolerance of the loop-loop interactions to lateral deformation provides the capacity for high-curvature bending without breaking. On the other hand, the local molecular architecture that surrounds these connecting loops contributes to the overall rigidity. Interprotofilament interactions in the seam region are similar to those in the normal helical regions, suggesting that the existence of the seam does not significantly affect the mechanical properties of microtubules.
History
DepositionApr 22, 2010-
Header (metadata) releaseMay 5, 2010-
Map releaseAug 31, 2010-
UpdateNov 2, 2010-
Current statusNov 2, 2010Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5196_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5196.map.gz / Format: CCP4 / Size: 17.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructural map of MT 16-4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.03 Å/pix.
x 120 pix.
= 243.6 Å		2.03 Å/pix.
x 200 pix.
= 406. Å		2.03 Å/pix.
x 200 pix.
= 406. 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: 2.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.75 / Movie #1: 2.6
Minimum - Maximum-5.9462 - 8.442209999999999
Average (Standard dev.)0.0010488 (±1.50355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200120
Spacing200200120
CellA: 406 Å / B: 406 Å / C: 243.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.032.032.03
M x/y/z200200120
origin x/y/z0.0000.0000.000
length x/y/z406.000406.000243.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200120
D min/max/mean-5.9468.4420.001

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Supplemental data

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Sample components

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Entire : The microtubule containing 16 protofilaments

EntireName: The microtubule containing 16 protofilaments
Components
  • Sample: The microtubule containing 16 protofilaments
  • Protein or peptide: microtubule with 16 protofilaments

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Supramolecule #1000: The microtubule containing 16 protofilaments

SupramoleculeName: The microtubule containing 16 protofilaments / type: sample / ID: 1000
Oligomeric state: The 16-protofilament microtubule forms a helical structure
Number unique components: 2

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Macromolecule #1: microtubule with 16 protofilaments

MacromoleculeName: microtubule with 16 protofilaments / type: protein_or_peptide / ID: 1 / Name.synonym: MT 16-4
Details: Microtubule with 16 protofilaments and 4-start helical structure
Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: Bovine / Tissue: Brain
Molecular weightExperimental: 50 MDa / Theoretical: 50 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8 / Details: 25mM Pipes, 25mM NaCl, 2mM MgCl2, 1mM EGTA
GridDetails: 300 mesh copper grid covered with home-made carbon films
VitrificationCryogen name: ETHANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made plunger / Method: Blot for 2 second before plunging

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Electron microscopy

MicroscopeJEOL 4000EX
TemperatureAverage: 105 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 400,000 times magnification
Legacy - Electron beam tilt params: 0
DateJul 12, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 425 / Average electron dose: 15 e/Å2
Details: The micrographs were digitized with a customized robotic scanning system that uses a Nikon Coolpix 8000 scanner
Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsWith addition of Taxol or Taxotere for microtubule stabilization
CTF correctionDetails: Each micrograph
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: OTHER / Software - Name: SPIDER

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Atomic model buiding 1

Initial modelPDB ID:

1jff

SoftwareName: Chimera
DetailsProtocol: Rigid Body. A homology model was generated for the missing region in 1JFF from residues 35 to 60 in alpha-tubulin (by N. Banavali). The tubulin dimer structure was fitted into the density maps using the rigid body fitting function in Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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