Journal: Cell Rep / Year: 2013 Title: Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases. Authors: Ana B Asenjo / Chandrima Chatterjee / Dongyan Tan / Vania DePaoli / William J Rice / Ruben Diaz-Avalos / Mariena Silvestry / Hernando Sosa / Abstract: To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron ...To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron microscopy (EM) and fluorescence polarization microscopy. We report a nanometer-resolution (1.1 nm) cryo-EM three-dimensional structure of the KLP10A head domain (KLP10AHD) bound to curved tubulin. We found that binding of KLP10AHD induces a distinct tubulin configuration with displacement (shear) between tubulin subunits in addition to curvature. In this configuration, the kinesin-binding site differs from that in straight tubulin, providing an explanation for the distinct interaction modes of kinesin-13s with the microtubule lattice or its ends. The KLP10AHD-tubulin interface comprises three areas of interaction, suggesting a crossbow-type tubulin-bending mechanism. These areas include the kinesin-13 family conserved KVD residues, and as predicted from the crossbow model, mutating these residues changes the orientation and mobility of KLP10AHDs interacting with the microtubule.
History
Deposition
Jan 9, 2013
-
Header (metadata) release
Feb 20, 2013
-
Map release
Mar 6, 2013
-
Update
Apr 10, 2013
-
Current status
Apr 10, 2013
Processing site: RCSB / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
A: 580.0 Å / B: 580.0 Å / C: 160.0 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
2
2
2
M x/y/z
290
290
80
origin x/y/z
0.000
0.000
0.000
length x/y/z
580.000
580.000
160.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-50
29
166
NX/NY/NZ
106
122
134
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
290
290
80
D min/max/mean
-0.124
0.159
0.000
-
Supplemental data
-
Sample components
-
Entire : kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...
Entire
Name: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Components
Sample: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Protein or peptide: KLP10A
Protein or peptide: Tubulin alpha-1A chain
Protein or peptide: Tubulin beta-2B chain
-
Supramolecule #1000: kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...
Supramolecule
Name: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 2
-
Macromolecule #1: KLP10A
Macromolecule
Name: KLP10A / type: protein_or_peptide / ID: 1 / Name.synonym: kinesin-13, kinI / Details: KLP10A head domain / Number of copies: 1 / Recombinant expression: Yes
Source (natural)
Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly / Location in cell: cytoplasm
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi