Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex

REL PDBe PDBe PDBe 2016-02-18 2016-03-09 2016-06-29 2016-07-13 Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex Verba KA Wang RYR Arakawa A Liu Y Shirouzu M Yokoyama S Agard DA Hsp90, Cdc37, Cdk4, chaperone, kinase, unfolding Verba KA Wang RYR Arakawa A Liu Y Shirouzu M Yokoyama S Agard DA Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase SCIENCE 352 1542 1547 2016 27339980 doi:10.1126/science.aaf5023 Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 Complex of Human Hsp90 beta, human Cdc37 and human Cdk4

All three proteins were co-expressed in Sf9 cells.

One Hsp90 homodimer binds to one Cdc37 and one Cdk4 3 0.245 0.245 As cloned, verified by SDS-PAGE Heat Shock Protein HSP 90 beta Homo sapiens Human cytoplasm 0.083 2 Dimer true Spodoptera frugiperda pFastBacHT P08238 GO:0000052 IPR001404 Hsp90 co-chaperone Cdc37 Homo sapiens Human throughout 0.0445 1 true Spodoptera frugiperda pFastBacHT Q16543 GO:0000002 Cyclin-dependent kinase 4 Homo sapiens Human throughout 0.0337 1 true Spodoptera frugiperda pFastBacHT P11802 GO:0000038 IPR000719 singleParticle particle 0.27 7.5

20mM Tris-HCl (pH 7.5), 150 mM NaCl, 10 mM KCl, 10 mM MgCl2, 20 mM Na2MoO4, 2mM DTT, 0.085mM DDM

Glow discharged for 30 sec, C-flat 400 mesh 1.2/1.3 thick carbon grids (Protochips)

ETHANE 90 95 FEI VITROBOT MARK III Single blot from 4 to 6 seconds, at 20C FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.4 3.8 22500.0 FEI TITAN KRIOS AUTOGRID HOLDER At high mag via FT. 2014-11-25 GATAN K2 SUMMIT (4k x 4k) 3718 44

38 frames, 7.6 seconds total exposure

Image stacks were corrected for motion and summed as described previously, resulting in binned sums (1.315A/pix). For particle picking the images were binned to 5.2A/pix and Gaussian bandpass filtered between 15A and 500A using EMAN2. SamViewer template based picking was then used to pick particles from all the micrographs, followed by manual review of all the picks. After such procedure 802877 particles were picked in total and extracted from images binned to 2.6A/pix. CTFFIND4 was used to estimate defocus parameters for all the images. Relion 1.4 was used for all the following steps unless noted otherwise. Reference free 2D classification into 300 classes for 75 iterations was performed followed by manual examination of the resulting class averages. Low resolution/signal to noise/feature class averages and contributing particles were discarded, resulting in 670000 particles left. The resulting particles were 3D classified into 4 classes resulting in two classes having high-resolution features (390000 particles). At this stage particles were extracted from 1.315A/pix micrographs and all the following processing was done with these particles. Using 3D Auto-refine in Relion 1.4, a reconstruction was obtained from 390000 particles resulting from 3D classification above (using highest resolution 3D class as initial model, low pass filtered to 20A). Using the resulting parameters, the particles were further drift corrected per particle and dose weighted using the Particle Polishing feature. The B-factor weighing curve was fit by a polynomial (with a rationale that such a curve should be smooth) and used to generate new weighting parameters for Particle Polishing, with which 390000 particles were then polished. All further data processing was done using the polished particles. Re-refinement of the 390000 particles after polishing yielded the map at about 4A resolution (determined using gold standard FSC in the PostProcessing tab). Raw particles were sharpened with a B-factor of -50, low pass filtered with Gaussian filter to 3A and the refinement was continued for 10 more iterations (until convergence) with these particles (the rationale was that due to extremely low noise levels of K2 direct detector, this would yield more accurate alignments due to presence of more high resolution data in the images). This reconstruction was not sharpened and was filtered based on the spherical mask FSC resolution, 5.6A. Otherwise it is the same as EMD-3338.

C1 5.6 OTHER Relion 388688 1 emd_3339.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 336.64 336.64 336.64 90.0 90.0 90.0 X Y Z -0.00403766 0.0220517 0.00001659 0.00061396 1.315 1.315 1.315 0.0057 AUTHOR Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337. This one is same as EMD-3337, but un-sharpened and filtered to 5.5A. This map has more coherent density for Cdk4 C-lobe.

::::EMDATABANK.org::::EMD-3339::::

5fwk A B E K RIGID BODY FIT Chimera

The model was built using Rosetta into EMD-3338 and its sister EMD-3337 (depending on the region), but was refined into the EMD-3337 map only. Then the resulting model was rigid body fit into this map in Chimera.

REAL

emd_3339.tif emd_3339_fsc.xml