8CI8: Nup98(298-327) fibril

Cryo-EM structure of the Nup98(298-327) fibril. Determined by electron microscopy at 2.67 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 2.67 Å
Organism: Homo sapiens
Chains: 25
Atoms: 3,430
Mol. weight: 75.86 kDa
Released: 21 Feb 2024

Explore 8CI8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CI8 contains 0 α-helices and 80 β-strands across 25 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, F, K, P and U: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	318-319	2	1
β-strand	322-325	4	2

Chains B, G, L, Q and V: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	306-309	4	3
β-strand	312-322	11	4

Chains C, H, M, R and W: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	300-301	2	5
β-strand	304-309	6	6
β-strand	312-313	2	7
β-strand	316-319	4	8
β-strand	322-323	2	9

Chains D and I: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	301-302	2	10
β-strand	305	1	11
β-strand	308-309	2	12
β-strand	312-315	4	13
β-strand	318-321	4	14

Chains E, J, O, T and Y: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	301-302	2	15
β-strand	306	1	16

Chains N, S and X: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	301-302	2	10
β-strand	305	1	11
β-strand	308-309	2	12
β-strand	312-315	4	13
β-strand	318-323	6	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear pore complex protein Nup98	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y	protein	30	Homo sapiens	P52948 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y), FASTA

>8CI8_1 Nuclear pore complex protein Nup98 (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y)
TGFSFGNTSTIGQPSTNTMGLFGVTQASQP

Primary citation

Impact of distinct FG nucleoporin repeats on Nup98 self-association. Ibanez de Opakua, A., Pantoja, C.F., Cima-Omori, M.S. et al. Nat Commun (2024) 15:3797-3797. DOI 10.1038/s41467-024-48194-4 · PubMed

Other PDB entries of the same protein (UniProt P52948 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BZM 0.9 Å, GFGNFGTS from low-complexity/FG repeat domain of Nup98, residues 116-123
9PLM 1.32 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-021)
32QT 1.47 Å, Human NUP98 APD (SG P21)
32QU 1.5 Å, Human NUP98 APD (SG P41212)
9PLL 1.6 Å, TRIM21-NUP98 Molecular Glue Complex (MAN-056)
3MMY 1.65 Å, Structural and functional analysis of the interaction between the nucleoporin Nup98 and…
2Q5X 1.9 Å, Crystal Structure of the C-terminal domain of hNup98
7MNI 2.0 Å, Crystal structure of the N-terminal domain of NUP88 in complex with NUP98 C-terminal…
2Q5Y 2.3 Å, Crystal Structure of the C-terminal domain of hNup98
7F90 2.39 Å, Crystal structure of SARS auxiliary protein in complex with human nuclear protein
7VPG 2.49 Å, Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human…
7Q64 2.76 Å, Cryo-em structure of the Nup98 fibril polymorph 1

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