REL RCSB RCSB RCSB 2014-11-18 2014-11-26 2014-11-26 2016-02-10 High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation Shang ZG Zhou KF Xu C Csencsits R Cochran JC Sindelar CV molecular motors, kinesin, myosin, microtubules, cytoskeletal motors Shang ZG Zhou KF Xu C Csencsits R Cochran JC Sindelar CV High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation. eLife 3 e04686 e04686 2014 25415053 doi:10.7554/eLife.04686 3j8x FULLOVERLAP Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket. One monomer of kinesin binds to one heterodimer of tubulin 2 0.135 monomeric kinesin-1A Homo sapiens Human 0.038
K349
1 monomer true Escherichia coli BL21(DE3) pHB40p tubulin Sus scrofa pig heterodimer false helical filament 6.8
25 mM PIPES, 25 mM NaCl, 2 mM MgCl2, 1 mM EGTA
300 mesh copper grid with homemade holey carbon
 ETHANE HOMEMADE PLUNGER FEI TECNAI F30 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.0 1.0 2.5 130000.0 GATAN LIQUID NITROGEN
8K x 8K Super-resolution mode was used; 10 frames total were collected.
2013-04-15 GATAN K2 (4k x 4k) 15
Initial alignment was done using customized SPIDER scripts. Reconstruction and subsequent refinement was done by FREALIGN.
9.455 25.77 C1 OTHER 5.0 OTHER SPIDER, FREALIGN
Approximately 140,000 asymmetric units were averaged in the final reconstruction.
done within FREALIGN
 emd_6187.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 96 -128 -128 -58 256 256 96 509.44 509.44 191.04001 90.0 90.0 90.0 X Y Z -0.02259131 0.05996572 0.00012049 0.00745614 1.99 1.99 1.9900001 0.02 AUTHOR Microtubule decorated with monomeric human kinesin (K349 construct) having an empty nucleotide pocket.
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 4HNA K A B FLEXIBLE FIT MDFF
MDFF was performed using explicit solvation, after placing active-site water coordinates identified in high-resolution crystal structures of kinesin's ATP-like state. Side chains were removed from the MDFF target potential. Following several equilibration steps, the relative strength of the EM map potential (GSCALE term) was slowly increased from 0 to 1 over the course of 10 nanoseconds. The t = 1.4 ns time point was selected to represent the final fitted model, based on the approximate convergence of the RMSD from the starting structure.
RMSD from the starting structure was monitored for convergence REAL