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- EMDB-1428: A lever-arm rotation drives motility of the minus-end-directed ki... -

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Basic information

Database: EMDB / ID: 1428
TitleA lever-arm rotation drives motility of the minus-end-directed kinesin Ncd.
Map dataNcd in its ATP bound, AMPPNP, state on 15 filament microtubules
Samplenon-claret disjunction atp, amppnp, state:
tubulin / ncd
SourceBos taurus (cattle)
Methodhelical reconstruction / cryo EM / 18 Å resolution
AuthorsEndres NF / Yoshioka C / Milligan RA / Vale RD
CitationJournal: Nature / Year: 2006
Title: A lever-arm rotation drives motility of the minus-end-directed kinesin Ncd.
Authors: Nicholas F Endres / Craig Yoshioka / Ronald A Milligan / Ronald D Vale
DateDeposition: Sep 19, 2007 / Header (metadata) release: Sep 19, 2007 / Map release: Sep 19, 2007 / Last update: May 26, 2011

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 6.54
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 6.54
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_1428.map.gz (map file in CCP4 format, 2910 KB)
Projections & slices

Image control

AxesZ (Sec.)X (Row.)Y (Col.)
73 pix
5 Å/pix.
= 365. Å
101 pix
5 Å/pix.
= 505. Å
101 pix
5 Å/pix.
= 505. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Contour Level:29.7, 6.54 (movie #1):
Minimum - Maximum-33.1489 - 45.8508
Average (Standard dev.)2.31237 (12.2871)


Space Group Number1
Map Geometry
Axis orderYXZ
CellA: 505 Å / B: 505 Å / C: 365 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z555
M x/y/z10110173
origin x/y/z0.0000.0000.000
length x/y/z505.000505.000365.000
start NX/NY/NZ000
MAP C/R/S213
start NC/NR/NS000
D min/max/mean-33.14945.8512.312

Supplemental data

Sample components

Entire non-claret disjunction atp, amppnp, state

EntireName: non-claret disjunction atp, amppnp, state
Oligomeric State: Motors bound to 15 protofilament helical microtubules
Number of components: 2

Component #1: protein, tubulin

ProteinName: tubulin / Oligomeric Details: helical 15 protofilaments / Recombinant expression: Yes
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Bos taurus (cattle)
Source (natural)Organ or tissue: brain

Component #2: protein, ncd

ProteinName: ncd / Oligomeric Details: Dimer / Recombinant expression: Yes / Number of Copies: 2
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET-17b plasmid Invitrogen

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersHand: RIGHT HANDED
Sample solutionSpecimen conc.: 10 mg/ml
Buffer solution: 25 mM MOPS (pH 7.25), 100 mM NaCl, 2 mM MgCl2, 1 mM EGTA and 1 mM dithiothreitol, 5mg/ml tubulin, 5mM AMPPNP
pH: 7.4
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 90 % / Method: 3 sec blot / Details: Vitrification instrument: Vitrobot

Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionScanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: phoelix / Resolution: 18 Å / Resolution method: phase overplots

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