2023-10-11 REL RCSB RCSB RCSB 2023-06-24 2023-10-11 2023-10-11 2023-10-11 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM45377 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH P41 GM109824 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH R01 GM112108 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) NIH GM117212 United States Lumenal ring of the isolated yeast NPC Akey CW Echeverria I Ouch C Fernandez-Martinez J Rout MP nuclear pore complex, nucleocytoplasmic transport, nucleoporin, membrane protein, TRANSPORT PROTEIN Akey CW Echeverria I Ouch C Nudelman I Shi Y Wang J Chait BT Sali A Fernandez-Martinez J Rout MP Implications of a multiscale structure of the yeast nuclear pore complex. Mol.Cell US 83 3283 3302.e5 2023 37738963 doi:10.1016/j.molcel.2023.08.025 1097-2765 2168 MOCEFL EMD-41117 other EM volume
Pom34-Pom152 membrane attachment site yeast NPC
 EMD-41119 other EM volume
Cytoplasmic outer ring of the yeast NPC
 EMD-41120 other EM volume
Central transporter/plug yeast NPC
 EMD-41121 other EM volume
Double outer ring connectors of the yeast NPC
 EMD-41122 other EM volume
Connectors in cytoplasmic outer ring of yeast NPC
 EMD-41123 other EM volume
Composite multiscale structure of the yeast NPC
 EMD-41285 other EM volume
Double nuclear outer ring of Nup84-complexes from the yeast NPC
 EMD-41114 other EM volume
Full nuclear double outer ring of the yeast NPC
 EMD-41300 other EM volume
Inner spoke ring of the yeast NPC
 Lumenal rig of Nuclear Pore Complex Lumenal rig of Nuclear Pore Complex 0
Protein A tagged Mlp1 pullout of NPC
Saccharomyces cerevisiae MATa ade2-1 ura3-1 his3-11,15 trp1-1 leu2-3,112 can1-100 MLP1-PPX-ProteinA::HIS5 nucleus nuclear envelope singleParticle particle 0.1 7.5
20mM HEPES,50mM Potassium acetate,20mM NaCl,2mM MgCl2,1mM DTT
 Quantifoil R2/2 COPPER 400 CARBON HOLEY ARRAY 5.0 GLOW DISCHARGE OTHER ETHANE 100 283 FEI VITROBOT MARK III
One step affinity purified with NPC
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 3.5 37651.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20
Preliminary grid screening done manually with individual images of low magnification montages of candidate meshes.
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 2-40 1 4015 40.0
3218 images retained after triage
 1 85322
from Multibody with 2x protomer
low resolution composite 3D map of spoke and lumenal ring
 C2 FOURIER SPACE 14.7 FSC 0.143 CUT-OFF RELION 3.0.7
half maps were masked to remove contaminating density from the Multibody step.
85322 MAXIMUM LIKELIHOOD RELION 3.0.7
C1 symmetry in refinemet, C2 enforced 3D reference.
 MAXIMUM LIKELIHOOD RELION 3.0 7
C1 symmetry with appropriate mask in stepwise refinements gradually excluding proximal regions of the spoke used to refine with 2.5x Multibody
 RELION 3.0.7 emd_41116.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.66977376 1.8079556 0.005565968 0.06463531 2.66 2.66 2.66 0.73 AUTHOR Main map reconstructed from Multibody volume Other experimental model
none
 OTHER
The 2x protomer was fitted together to form a complete c8 lumenal ring with imposed 2-fold symmetry.
cross correlation REAL emd_41116_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 957.60004 957.60004 957.60004 90.0 90.0 90.0 X Y Z -0.09040683 0.13408172 0.000082991224 0.00223375 5.32 5.32 5.32 AUTHOR multibody half map emd_41116_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 957.60004 957.60004 957.60004 90.0 90.0 90.0 X Y Z -0.6407663 0.9442973 0.00052067835 0.014714022 5.32 5.32 5.32 AUTHOR post processed multibody volume bf -300 local resolution box 50 emd_41116_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 957.60004 957.60004 957.60004 90.0 90.0 90.0 X Y Z -0.08875357 0.14568102 0.00008656707 0.0022440047 5.32 5.32 5.32 AUTHOR multibody half map emd_41116_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.105367035 0.2606998 0.0002921562 0.004438549 2.66 2.66 2.66 AUTHOR half map full D8 lumenal ring emd_41116_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 1276.8 1276.8 1276.8 90.0 90.0 90.0 X Y Z -0.11431952 0.25215295 0.00028008968 0.004413265 2.66 2.66 2.66 AUTHOR half map full D8 lumenal ring