functional orthologs of Nup93 and the Alpha-
Fold model. The EM maps also allow identifi-
cation of protein-protein interfaces mediated by
Nup93 (figs. S11, S12, and S14).
With one Nup93-ACE1 assigned to the bridge
domain and two Nup93a5 helices identified to
be inserted into the CTD of Nup205 molecules,
we investigated whether a second copy of
Nup93-ACE1 was present within the CR sub-
unit. The current molecular model left a chunk
of unassigned density spanning the Nup107-I
from one subunit and Nup205-O from the
adjacent subunit that adopts a similar shape as
those of the bridge domain. Local refinements
focusing on this chunk of density revealed that
a second copy of Nup93-ACE1 was indeed
present in the CR subunit. Direct docking of
the model of Nup93-ACE1-O into this region
resulted in a nearly perfect match (fig. S10F).
Modeling and structural analyses of other
nucleoporins were facilitated by sequence
alignment ( 55 , 56 ) of functional orthologs of
the structurally defined CR components and
AlphaFold-predicted models. Overall, the final
model of the CR subunit includes the inner and
outer Y complexes, two Nup205 molecules, five
Nup358 clamps, two Nup93 molecules, and one
copy each of Nup88, Nup98/X, and Nup155.
This model includes 19,037 amino acids in 749
a-helices and 380b-strands (tables S2 and S3).
The final model was refined using Phenix ( 50 )
with secondary structure restraints and vali-
dated through examination of the Molprobity
scores and statistics of the Ramachandran plots
( 57 ) (table S1). Together with the EM density
map, this model allows structural analysis of
Nup205 (Fig. 3), Nup93 (Fig. 4 and figs. S10, S11,
S12,andS14),andNup358(Fig.5andfigs.S13
and S14) clamps. In addition, the final model
provides a basis for the identification of inter-
subunit protein-protein interfaces (fig. S15) and
structural comparisons among Y complexes
from various species (fig. S16) and between
individual components of the CR (fig. S17 and
table S4).
The figures for structures and maps were
generated using Pymol,Chimera, or ChimeraX
( 51 , 58 ). Sequence alignments were done in
Clustal Omega ( 55 )andESPript3.0( 56 ).
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RESEARCH | STRUCTURE OF THE NUCLEAR PORE