1KO6: Nuclear Pore Complex Protein Nup98

Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98. Determined by X-ray diffraction at 3.0 Å resolution. Released 4 Sept 2002.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,480
Mol. weight: 56.63 kDa
Released: 4 Sept 2002

Explore 1KO6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1KO6 contains 12 α-helices and 26 β-strands across 4 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.

Chain A: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	718	1	1
β-strand	724-727	4	2
α-helix	730-736	7
β-strand	744-745	2	3
β-strand	748-752	5	2
β-strand	756-760	5	2
β-strand	764-765	2	3
β-strand	770	1	1
α-helix	771-774	4
β-strand	775-778	4	4
β-strand	781-784	4	4
α-helix	791-793	3
β-strand	802-806	5	2
α-helix	823-829	7
α-helix	831-841	11
β-strand	845-850	6	2
α-helix	851-853	3
β-strand	855-860	6	2

Chains B and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	866-867	2	4

Chain C: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	724-727	4	5
α-helix	732-735	4
β-strand	744	1	6
β-strand	748-752	5	5
β-strand	756-760	5	5
β-strand	765	1	6
α-helix	771-774	4
β-strand	775-778	4	7
β-strand	781-784	4	7
β-strand	794	1	8
β-strand	796	1	8
α-helix	797-799	3
β-strand	802-806	5	5
α-helix	823-828	6
α-helix	831-841	11
β-strand	845-850	6	5
α-helix	851-853	3
β-strand	855-860	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear Pore Complex Protein Nup98	A, C	protein	187	Homo sapiens	P52948 (AlphaFold model)
Nuclear Pore Complex Protein Nup98	B, D	protein	64	Homo sapiens	P52948 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1KO6_1 Nuclear Pore Complex Protein Nup98 (chains A, C)
MAALRNGLEGSSEETSFHDESLQDDREEIENNSYHMHPAGIILTKVGYYTIPSMDDLAKI
TNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGE
GLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSW
VFKVSHF

Sequence of entity 2 (B, D), FASTA

>1KO6_2 Nuclear Pore Complex Protein Nup98 (chains B, D)
SKYGLQDSDEEEEEHPSKTSTKKLKTAPLPPASQTTPLQMALNGKPAPPPQVEKKGQLEH
HHHH

Primary citation

The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98. Hodel, A.E., Hodel, M.R., Griffis, E.R. et al. Mol Cell (2002) 10:347-358. DOI 10.1016/S1097-2765(02)00589-0 · 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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