2Q5Y: C-terminal domain of hNup98

Crystal Structure of the C-terminal domain of hNup98. Determined by X-ray diffraction at 2.3 Å resolution. Released 14 Oct 2008.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,526
Mol. weight: 36.03 kDa
Released: 14 Oct 2008

Explore 2Q5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2Q5Y contains 10 α-helices and 25 β-strands across 3 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	730-735	6
β-strand	744-752	9	2
β-strand	756-765	10	2
β-strand	770	1	1
α-helix	771-774	4
β-strand	775-778	4	3
β-strand	781-784	4	3
α-helix	788-790	3
α-helix	792-793	2
β-strand	802-806	5	2
β-strand	812	1	4
β-strand	819	1	4
α-helix	823-828	6
α-helix	831-841	11
β-strand	845-850	6	2
β-strand	855-860	6	2

Chain C: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	718	1	5
β-strand	724-727	4	6
α-helix	730-735	6
β-strand	744-752	9	6
β-strand	756-765	10	6
β-strand	770	1	5
α-helix	771-774	4
β-strand	775-778	4	7
β-strand	781-784	4	7
β-strand	802-806	5	6
β-strand	812	1	8
β-strand	819	1	8
α-helix	823-828	6
α-helix	831-841	11
β-strand	845-850	6	6
β-strand	855-860	6	6

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	867	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear pore complex protein Nup98	A, C	protein	152	Homo sapiens	P52948 (AlphaFold model)
Nuclear pore complex protein Nup96	B, D	protein	7		P52948 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2Q5Y_1 Nuclear pore complex protein Nup98 (chains A, C)
MHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNL
DDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINY
EGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF

Sequence of entity 2 (B, D), FASTA

>2Q5Y_2 Nuclear pore complex protein Nup96 (chains B, D)
SKYGLQD

Primary citation

Structural constraints on autoprocessing of the human nucleoporin Nup98. Sun, Y., Guo, H.C. Protein Sci (2008) 17:494-505. DOI 10.1110/ps.073311808 · 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…
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
7Q64 2.76 Å, Cryo-em structure of the Nup98 fibril polymorph 1

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