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- EMDB-10131: MKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) p... -

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Basic information

Entry
Database: EMDB / ID: EMD-10131
TitleMKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) processed with MiRP (Microtubule Relion-based Pipeline)
Map dataMKLP2 (ADPAlFx state) decorated 13PF microtubule: symmetrised asymmetric unit density from MiRP processing
Sample
  • Complex: Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx
    • Complex: Tubulin alpha and beta chains
    • Complex: Kinesin-like protein KIF20A
Biological speciesBos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsCook AC / Manka SW / Wang S / Moores CA / Atherton J
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/R000352/1 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Medical Research Council (United Kingdom)MR/J003867/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/L014211/1 United Kingdom
Wellcome Trust101488/Z/13/Z United Kingdom
CitationJournal: Elife / Year: 2017
Title: The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.
Authors: Joseph Atherton / I-Mei Yu / Alexander Cook / Joseph M Muretta / Agnel Joseph / Jennifer Major / Yannick Sourigues / Jeffrey Clause / Maya Topf / Steven S Rosenfeld / Anne Houdusse / Carolyn A Moores /
Abstract: MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% ...MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% identity) and size (~40% larger) compared to other kinesins. Using cryo-electron microscopy and biophysical assays, we have undertaken a mechanochemical dissection of the microtubule-bound MKLP2 motor domain during its ATPase cycle, and show that many facets of its mechanism are distinct from other kinesins. While the MKLP2 neck-linker is directed towards the microtubule plus-end in an ATP-like state, it does not fully dock along the motor domain. Furthermore, the footprint of the MKLP2 motor domain on the MT surface is altered compared to motile kinesins, and enhanced by kinesin-6-specific sequences. The conformation of the highly extended loop6 insertion characteristic of kinesin-6s is nucleotide-independent and does not contact the MT surface. Our results emphasize the role of family-specific insertions in modulating kinesin motor function.
History
DepositionJul 18, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10131.png

Downloads & links

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Map

FileDownload / File: emd_10131.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMKLP2 (ADPAlFx state) decorated 13PF microtubule: symmetrised asymmetric unit density from MiRP processing
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.53 Å/pix.
x 109 pix.
= 167.206 Å		1.53 Å/pix.
x 103 pix.
= 158.002 Å		1.53 Å/pix.
x 80 pix.
= 122.72 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: 1.534 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.15499362 - 0.29427066
Average (Standard dev.)0.001958117 (±0.01719634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin83192157
Dimensions10380109
Spacing80103109
CellA: 122.72 Å / B: 158.002 Å / C: 167.20601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5341.5341.534
M x/y/z80103109
origin x/y/z0.0000.0000.000
length x/y/z122.720158.002167.206
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS19283157
NC/NR/NS80103109
D min/max/mean-0.1550.2940.002

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Supplemental data

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Additional map: MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole...

Fileemd_10131_additional.map
AnnotationMKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole microtubule density from MiRP processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole...

Fileemd_10131_additional_1.map
AnnotationMKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole microtubule density from MiRP processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 13pf microtubule with bound MKLP2 motor domain in the ...

EntireName: Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx
Components
  • Complex: Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx
    • Complex: Tubulin alpha and beta chains
    • Complex: Kinesin-like protein KIF20A

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Supramolecule #1: Complex of 13pf microtubule with bound MKLP2 motor domain in the ...

SupramoleculeName: Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Microtubule bound to taxol

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Supramolecule #2: Tubulin alpha and beta chains

SupramoleculeName: Tubulin alpha and beta chains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3 / Details: Microtubule bound to taxol
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #3: Kinesin-like protein KIF20A

SupramoleculeName: Kinesin-like protein KIF20A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1 / Details: Microtubule bound to taxol
Source (natural)Organism: Mus musculus (house mouse)
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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Details: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: Following the MiRP pipeline / Number images used: 14411
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION / Details: Following the MiRP pipeline
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION / Details: Following the MiRP pipeline
Final 3D classificationSoftware - Name: RELION / Details: Following the MiRP pipeline

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Atomic model buiding 1

Initial modelPDB ID:

5nd4

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