7Q64: Nup98 fibril polymorph 1

Cryo-em structure of the Nup98 fibril polymorph 1. Determined by electron microscopy at 2.76 Å resolution. Released 12 Oct 2022.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 30
Atoms: 7,810
Mol. weight: 120.16 kDa
Released: 12 Oct 2022

Explore 7Q64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q64 contains 0 α-helices and 160 β-strands across 30 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, C, d, F, I, L, O, R, U and X: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	90-94	5	13
β-strand	97-101	5	14
β-strand	104-111	8	15
β-strand	115-120	6	16

Chains A, b, D, G, J, M, P, S, V and Y: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	88	1	1
β-strand	92-96	5	2
β-strand	100-104	5	3
β-strand	110	1	4
β-strand	115	1	5
β-strand	120-123	4	6

Chains B, c, E, H, K, N, Q, T, W and Z: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	88-89	2	7
β-strand	94-96	3	8
β-strand	100-101	2	9
β-strand	104-107	4	10
β-strand	111-112	2	11
β-strand	115	1	12

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, Z, a, b, c, d	protein	40	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, Z, a, b, c, d), FASTA

>7Q64_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, Z, a, b, c, d)
TGTANTLFGTASTGTSLFSSQNNAFAQNKPTGFGNFGTST

Primary citation

Molecular interactions of FG nucleoporin repeats at high resolution. Ibanez de Opakua, A., Geraets, J.A., Frieg, B. et al. Nat Chem (2022) 14:1278-1285. DOI 10.1038/s41557-022-01035-7 · 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…
8CI8 2.67 Å, Cryo-EM structure of the Nup98(298-327) fibril

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