[English] 日本語
Yorodumi- EMDB-10131: MKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10131 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | MKLP2-decocrated 13 protofilament microtubule (ADP.Al.Fx state) processed with MiRP (Microtubule Relion-based Pipeline) | ||||||||||||||||||
Map data | MKLP2 (ADPAlFx state) decorated 13PF microtubule: symmetrised asymmetric unit density from MiRP processing | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Biological species | Bos taurus (cattle) / Mus musculus (house mouse) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
Authors | Cook AC / Manka SW / Wang S / Moores CA / Atherton J | ||||||||||||||||||
Funding support | United Kingdom, 5 items
| ||||||||||||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10131.map.gz | 794.5 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10131-v30.xml emd-10131.xml | 16 KB 16 KB | Display Display | EMDB header |
Images | emd_10131.png | 156 KB | ||
Others | emd_10131_additional.map.gz emd_10131_additional_1.map.gz | 285.2 MB 285.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10131 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10131 | HTTPS FTP |
-Related structure data
Related structure data | 4862C 6rf8C C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10796 (Title: A microtubule RELION-based pipeline for cryo-EM image processing Data size: 256.7 Data #1: Movies of microtubules decorated with MKLP2 motor domain (ADPAlFx bound) [micrographs - single frame] Data #2: Single-frames of microtubules decorated with MKLP2 motor domain (ADPAlFx bound) [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_10131.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MKLP2 (ADPAlFx state) decorated 13PF microtubule: symmetrised asymmetric unit density from MiRP processing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.534 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole...
File | emd_10131_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole microtubule density from MiRP processing | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole...
File | emd_10131_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | MKLP2 (ADPAlFx state) decorated 13PF microtubule: C1 whole microtubule density from MiRP processing | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of 13pf microtubule with bound MKLP2 motor domain in the ...
Entire | Name: Complex of 13pf microtubule with bound MKLP2 motor domain in the presence of ADP.AlFx |
---|---|
Components |
|
-Supramolecule #1: Complex of 13pf microtubule with bound MKLP2 motor domain in the ...
Supramolecule | Name: 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 |
---|
-Supramolecule #2: Tubulin alpha and beta chains
Supramolecule | Name: 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 (cattle) |
-Supramolecule #3: Kinesin-like protein KIF20A
Supramolecule | Name: 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 expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf / Details: RELION |
---|---|
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION / Details: Following the MiRP pipeline |
Final 3D classification | Software - Name: RELION / Details: Following the MiRP pipeline |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION / Details: Following the MiRP pipeline |
Final reconstruction | Resolution.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 |
-Atomic model buiding 1
Initial model | PDB ID: |
---|