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- EMDB-8547: Kinesin-1 Binding Microtubules with ADP-AlFx in a One-head-bound ... -

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Basic information

Entry
Database: EMDB / ID: 8547
TitleKinesin-1 Binding Microtubules with ADP-AlFx in a One-head-bound State (low-pass filtered to 8.5 angstrom)
Map data
SampleKinesin-1 (1-420) on microtubules with ADP-AlFx in a one-head-bound state:
Kinesin-1 / Alpha-tubulin / Beta-tubulinTubulin
SourceBos taurus (cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.7 Å resolution
AuthorsLiu D / Liu X / Shang Z / Sindelar CV
CitationJournal: Elife / Year: 2017
Title: Structural basis of cooperativity in kinesin revealed by 3D reconstruction of a two-head-bound state on microtubules.
Authors: Daifei Liu / Xueqi Liu / Zhiguo Shang / Charles V Sindelar
DateDeposition: Jan 12, 2017 / Header (metadata) release: Jan 18, 2017 / Map release: Jan 25, 2017 / Last update: Feb 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.046
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.046
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.046
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8547.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
2.06 Å/pix.
= 721. Å
350 pix
2.06 Å/pix.
= 721. Å
350 pix
2.06 Å/pix.
= 721. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density
Contour Level:0.046 (by author), 0.046 (movie #1):
Minimum - Maximum-0.024415813 - 0.1052176
Average (Standard dev.)-0.0010091908 (0.011948339)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions350350350
Origin-174.0-174.0-174.0
Limit175.0175.0175.0
Spacing350350350
CellA=B=C: 721.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z721.000721.000721.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-174-174-174
NC/NR/NS350350350
D min/max/mean-0.0240.105-0.001

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Supplemental data

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Sample components

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Entire Kinesin-1 (1-420) on microtubules with ADP-AlFx in a one-head-bou...

EntireName: Kinesin-1 (1-420) on microtubules with ADP-AlFx in a one-head-bound state
Number of components: 4

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Component #1: protein, Kinesin-1 (1-420) on microtubules with ADP-AlFx in a one...

ProteinName: Kinesin-1 (1-420) on microtubules with ADP-AlFx in a one-head-bound state
Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Component #2: protein, Kinesin-1

ProteinName: Kinesin-1 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Alpha-tubulin

ProteinName: Alpha-tubulin / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Component #4: protein, Beta-tubulin

ProteinName: Beta-tubulinTubulin / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 6.8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.65 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 44298
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF
Details: a modified version of frealign was used for reconstruction, kinesin dimer was masked before FSC calculation using half maps.

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