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- EMDB-20093: Cryo-EM reconstruction of the 'x1x' binding pattern in the low AD... -

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Basic information

Entry
Database: EMDB / ID: EMD-20093
TitleCryo-EM reconstruction of the 'x1x' binding pattern in the low ADP condition for dimeric kinesin-1 with a central bound site and flanking sites with either bound or empty occupancy
Map dataNone
Sample
  • Complex: Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-stabilized microtubules
Biological specieshomo s (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsCha HK / Debs G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteR01 GM 110530-01 United States
CitationJournal: To Be Published
Title: Structural Intermediates of the Dimeric Kinesin Stepping Cycle Revealed by Cryo-EM
Authors: Cha HK / Debs G / Liu X / Liu D / Sindelar CV
History
DepositionApr 12, 2019-
Header (metadata) releaseMay 1, 2019-
Map releaseApr 15, 2020-
UpdateApr 15, 2020-
Current statusApr 15, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20093.png

Downloads & links

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Map

FileDownload / File: emd_20093.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 420 pix.
= 559.86 Å		1.33 Å/pix.
x 420 pix.
= 559.86 Å		1.33 Å/pix.
x 420 pix.
= 559.86 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.023831775 - 0.07124587
Average (Standard dev.)0.00015149335 (±0.0037535448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 559.86 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3331.3331.333
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z559.860559.860559.860
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ460460460
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0240.0710.000

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Supplemental data

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Sample components

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Entire : Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-sta...

EntireName: Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-stabilized microtubules
Components
  • Complex: Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-stabilized microtubules

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Supramolecule #1: Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-sta...

SupramoleculeName: Dimeric kinesin-1 in the presence of 0.2uM ADP bound to taxol-stabilized microtubules
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: homo s (domestic cattle)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.65 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 123259
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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