Integrative Structure and Functional Anatomy of a Nuclear Pore Complex

2020-08-12 REL RCSB RCSB RCSB 2017-12-27 2018-02-14 2018-03-28 2020-08-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM083960 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM103314 United States National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) U54 DK107981 United States National Science Foundation (NSF, United States) GRF 1650113 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM080477 United States National Science Foundation (NSF, United States) CHE-1531823 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM112108 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) U54 GM103511 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P50 GM076547 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM080139 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM063834 United States Integrative Structure and Functional Anatomy of a Nuclear Pore Complex Kim SJ Fernandez-Martinez J Nudelman I Shi Y Zhang W Ludtke SJ Akey CW Chait BT Sali A Rout MP Kim SJ Fernandez-Martinez J Nudelman I Shi Y Zhang W Raveh B Herricks T Slaughter BD Hogan JA Upla P Chemmama IE Pellarin R Echeverria I Shivaraju M Chaudhury AS Wang J Williams R Unruh JR Greenberg CH Jacobs EY Yu Z de la Cruz MJ Mironska R Stokes DL Aitchison JD Jarrold MF Gerton JL Ludtke SJ Akey CW Chait BT Sali A Rout MP Integrative structure and functional anatomy of a nuclear pore complex. Nature UK 2018 29539637 doi:10.1038/nature26003 1476-4687 0006 NATUAS EMD-7321 associated EM volume Saccharomyces cerevisiae NPC (nuclear pore complex) Saccharomyces cerevisiae NPC (nuclear pore complex) 0 1

Affinity-purified isolated whole NPCs

Saccharomyces cerevisiae 87 subtomogramAveraging particle 0.3 7.4 20.0 HEPES-KOH 50.0 KC2H3O2 potassium acetate 2.0 MgCl2 magnesium chloride 20.0 NaCl sodium chloride 0.1 Tween-20 10.0 glycerol 1.0 DTT dithiothreitol Quantifoil R2/1 COPPER 300

A medium thick carbon film was used to support the NPCs over the holes. Before use, the grids were glow discharged in air, floated on 5 uL sample drops for 45 minutes and then washed by serial transfer on 4 x 20 micro-litre drops of sample buffer without glycerol.

ETHANE 100 293 FEI VITROBOT MARK III

Buffer on the grid was removed by blotting from the bottom with a tool that held a filter paper wedge, using access through the left-hand port. Then 2 micro-litre of freezing buffer was added to the grid from the right-hand port and the grid was plunge frozen in liquid ethane after blotting..

Sample isolated in one affinity step - pullout from frozen yeast cell grindate.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.001 4.6 7.5 9434.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN Titan-Krios equipped with a spherical aberration (Cs) corrector none GIF Quantum LS 1 20

The electron gun was an XFEG. A total of 253 tilt series were collected in steps between -60, 0 and 60 degrees in increments of 2.5 - 4 degrees for different tilt series. While the full tilt range was used for tomogram reconstruction, in the final subtomogram averaging step only data up to +/-45 degrees tilt from each sub-volume were included in the final average. A defocus range of -4.6 to -7.5 microns was used.

GATAN K2 SUMMIT (4k x 4k) INTEGRATING 3838 3710 1 3.0

The dose target for each tilt series was 90-100 electrons/angstrom squared and followed a cosine alpha dose curve with a flux of 20 electrons/pixel/second, and a dose of 3.5 electrons/angstrom squared for the zero tilt image.

1 C8 FOURIER SPACE 28.0 FSC 0.143 CUT-OFF EMAN2 2.1

The final map has been fully CTF corrected and filtered based on the estimated local resolution.

1864 121 6416 manual selection EMAN2 2.12 e2spt_boxer.py

A low pass filter of 100 Angstroms was applied to binned 3X SIRT tomograms prior to particle picking. Final unbinned sub-volumes of 300 x 300 x 300 were extracted from the original tomograms.

EMAN2 2.1

Phase flipping of tilted images with etomo in IMOD running in batchtomo mode. The final reconstruction used 1,864 (of the 6,416 initial) particles. Theoretical CTF curves for the mean defocus values present in the tomograms were averaged assuming 10% amplitude contrast. The reciprocal of this curve was then applied as a filter to the final uncorrected map.

OTHER EMAN2 e2spt_classaverage.py in theEMAN2 single particle tomography package

Iterative 3D alignment of sub-volumes to a reference volume, using the C8 symmetry of the NPC.

emd_7321.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 1590.0 1590.0 1590.0 90.0 90.0 90.0 X Y Z -0.059866104 0.1641967 0.002676172 0.011975752 5.3 5.3 5.3 0.015 AUTHOR ::::EMDATABANK.org::::EMD-7321:::: Integrative Structure and Functional Anatomy of a Nuclear Pore Complex OTHER

The integrative structure modeling protocol was scripted using the Python Modeling Interface (PMI) package, version 4d97507, a library for modeling macromolecular complexes based on our open-source Integrative Modeling Platform (IMP) package, version 2.6 (https://integrativemodeling.org)