1ko6

Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98

Method: X-RAY DIFFRACTION D_max: 71.1 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear Pore Complex Protein Nup98

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 678–863 Chain B； UniProt 864–920 Chain C； UniProt 678–863 Chain D； UniProt 864–920	Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 677-863) Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 864-920)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.75；300 K；MgCl, PEG8000, Tris, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 3.00 Å R-free 0.271

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1KO6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Q5X Crystal Structure of the C-terminal domain of hNup98 Deposited 2007-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 733–887（155 aa） Fragment：C-terminal domain, residues 733-887	Mutation：S881A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；296 K；4.5M sodium formate, pH 4.6, vapor diffusion, hanging drop, temperature 296K	Resolution 1.90 Å R-free 0.229
2Q5Y Crystal Structure of the C-terminal domain of hNup98 Deposited 2007-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 729–880（152 aa） Fragment：C-terminal domain, residues 729-880 Chain B 881–887（7 aa） Fragment：residues 881-887	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；296 K；0.1M Tris, 0.2M MgAc2, 22% PEG8000, microseeding, pH 8.1, vapor diffusion, hanging drop, temperature 296K	Resolution 2.30 Å R-free 0.260
2Q5Y Crystal Structure of the C-terminal domain of hNup98 Deposited 2007-06-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 729–880（152 aa） Fragment：C-terminal domain, residues 729-880 Chain D 881–887（7 aa） Fragment：residues 881-887	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；296 K；0.1M Tris, 0.2M MgAc2, 22% PEG8000, microseeding, pH 8.1, vapor diffusion, hanging drop, temperature 296K	Resolution 2.30 Å R-free 0.260
3MMY Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 Deposited 2010-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 158–213（56 aa） Fragment：UNP residues 158-213	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.237
3MMY Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 Deposited 2010-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 158–213（56 aa） Fragment：UNP residues 158-213	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.237
3MMY Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 Deposited 2010-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 158–213（56 aa） Fragment：UNP residues 158-213	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.237
3MMY Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1 Deposited 2010-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 158–213（56 aa） Fragment：UNP residues 158-213	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.65 Å R-free 0.237
4OWR Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair Rae1-Nup98 Deposited 2014-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 157–213（57 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.1 M HEPES pH 7.5, 11% PEG 10, 000, and 10% MPD	Resolution 3.15 Å R-free 0.289
5A9Q Human nuclear pore complex Deposited 2015-07-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 304 PDB declaration: 304-meric	Chain 5 881–1817（937 aa） Chain E 881–1817（937 aa） Chain N 881–1817（937 aa） Chain W 881–1817（937 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20MM TRIS, 0.2-0.4% TREHALOSE；pH 7.5；20MM TRIS, 0.2-0.4% TREHALOSE cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, INSTRUMENT- HOMEMADE PLUNGER,	Resolution 23.00 Å
6BZM GFGNFGTS from low-complexity/FG repeat domain of Nup98, residues 116-123 Deposited 2017-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 116–123（8 aa） Fragment：UNP residues 116-123 Chain B 116–123（8 aa） Fragment：UNP residues 116-123	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 9.5 cryo-EM vitrification conditions Cryogen ETHANE X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；0.1 M CHES, pH 9.5, 10% ethanol	Resolution 0.90 Å R-free 0.264
7F60 Crystal structure of auxiliary protein in complex with human nuclear protein Deposited 2021-06-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1817（1817 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；0.1m Bis-tris ph5.5,45%PEG4000	Resolution 2.85 Å R-free 0.276
7F60 Crystal structure of auxiliary protein in complex with human nuclear protein Deposited 2021-06-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–1817（1817 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；0.1m Bis-tris ph5.5,45%PEG4000	Resolution 2.85 Å R-free 0.276
7F90 Crystal structure of SARS auxiliary protein in complex with human nuclear protein Deposited 2021-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1817（1817 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；0.1m Bis-tris ph5.5,45%PEG4000	Resolution 2.39 Å R-free 0.258
7F90 Crystal structure of SARS auxiliary protein in complex with human nuclear protein Deposited 2021-07-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1817（1817 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；296 K；0.1m Bis-tris ph5.5,45%PEG4000	Resolution 2.39 Å R-free 0.258
7PEQ Model of the outer rings of the human nuclear pore complex Deposited 2021-08-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 288 PDB declaration: 288-meric	Chain AE 881–1817（937 aa） Chain BE 881–1817（937 aa） Chain CE 881–1817（937 aa） Chain DE 881–1817（937 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.	Resolution 35.00 Å
7Q64 Cryo-em structure of the Nup98 fibril polymorph 1 Deposited 2021-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 30 PDB declaration: 30-meric	Chain A 85–124（40 aa） Chain B 85–124（40 aa） Chain C 85–124（40 aa） Chain D 85–124（40 aa） Chain E 85–124（40 aa） Chain F 85–124（40 aa） Chain G 85–124（40 aa） Chain H 85–124（40 aa） Chain I 85–124（40 aa） Chain J 85–124（40 aa） Chain K 85–124（40 aa） Chain L 85–124（40 aa） Chain M 85–124（40 aa） Chain N 85–124（40 aa） Chain O 85–124（40 aa） Chain P 85–124（40 aa） Chain Q 85–124（40 aa） Chain R 85–124（40 aa） Chain S 85–124（40 aa） Chain T 85–124（40 aa） Chain U 85–124（40 aa） Chain V 85–124（40 aa） Chain W 85–124（40 aa） Chain X 85–124（40 aa） Chain Y 85–124（40 aa） Chain Z 85–124（40 aa） Chain a 85–124（40 aa） Chain b 85–124（40 aa） Chain c 85–124（40 aa） Chain d 85–124（40 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
7Q65 Cryo-em structure of the Nup98 fibril polymorph 2 Deposited 2021-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 22 PDB declaration: 22-meric	Chain A 85–124（40 aa） Chain B 85–124（40 aa） Chain C 85–124（40 aa） Chain D 85–124（40 aa） Chain E 85–124（40 aa） Chain F 85–124（40 aa） Chain G 85–124（40 aa） Chain H 85–124（40 aa） Chain I 85–124（40 aa） Chain J 85–124（40 aa） Chain K 85–124（40 aa） Chain L 85–124（40 aa） Chain M 85–124（40 aa） Chain N 85–124（40 aa） Chain O 85–124（40 aa） Chain P 85–124（40 aa） Chain Q 85–124（40 aa） Chain R 85–124（40 aa） Chain S 85–124（40 aa） Chain T 85–124（40 aa） Chain U 85–124（40 aa） Chain V 85–124（40 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
7Q66 Cryo-em structure of the Nup98 fibril polymorph 3 Deposited 2021-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 22 PDB declaration: 22-meric	Chain A 85–124（40 aa） Chain B 85–124（40 aa） Chain C 85–124（40 aa） Chain D 85–124（40 aa） Chain E 85–124（40 aa） Chain F 85–124（40 aa） Chain G 85–124（40 aa） Chain H 85–124（40 aa） Chain I 85–124（40 aa） Chain J 85–124（40 aa） Chain K 85–124（40 aa） Chain L 85–124（40 aa） Chain M 85–124（40 aa） Chain N 85–124（40 aa） Chain O 85–124（40 aa） Chain P 85–124（40 aa） Chain Q 85–124（40 aa） Chain R 85–124（40 aa） Chain S 85–124（40 aa） Chain T 85–124（40 aa） Chain U 85–124（40 aa） Chain V 85–124（40 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.79 Å
7Q67 Cryo-em structure of the Nup98 fibril polymorph 4 Deposited 2021-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 11 PDB declaration: undecameric	Chain A 85–124（40 aa） Chain B 85–124（40 aa） Chain C 85–124（40 aa） Chain D 85–124（40 aa） Chain E 85–124（40 aa） Chain F 85–124（40 aa） Chain G 85–124（40 aa） Chain H 85–124（40 aa） Chain I 85–124（40 aa） Chain J 85–124（40 aa） Chain K 85–124（40 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric	Chain M0 881–1817（937 aa） Chain M1 881–1817（937 aa） Chain M2 881–1817（937 aa） Chain M3 881–1817（937 aa） Chain U0 1–880（880 aa） Chain U1 1–880（880 aa） Chain U2 1–880（880 aa） Chain U3 1–880（880 aa） Chain U4 1–880（880 aa） Chain U5 1–880（880 aa） Chain U6 1–880（880 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 808 PDB declaration: 808-meric	Chain M0 881–1817（937 aa） Chain M1 881–1817（937 aa） Chain M2 881–1817（937 aa） Chain M3 881–1817（937 aa） Chain U0 1–880（880 aa） Chain U1 1–880（880 aa） Chain U2 1–880（880 aa） Chain U3 1–880（880 aa） Chain U4 1–880（880 aa） Chain U5 1–880（880 aa） Chain U6 1–880（880 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å
7VPG Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.49 Å R-free 0.231
7VPG Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.49 Å R-free 0.231
7VPG Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.49 Å R-free 0.231
7VPG Crystal structure of the C-terminal tail of SARS-CoV-1 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.49 Å R-free 0.231
7VPH Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.80 Å R-free 0.244
7VPH Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.80 Å R-free 0.244
7VPH Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.80 Å R-free 0.244
7VPH Crystal structure of the C-terminal tail of SARS-CoV-2 Orf6 complex with human nucleoporin pair Rae1-Nup98 Deposited 2021-10-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 158–213（56 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Sodium citrate pH 5.5, 20% PEG 3350	Resolution 2.80 Å R-free 0.244
8CI8 Cryo-EM structure of the Nup98(298-327) fibril Deposited 2023-02-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 25 PDB declaration: 25-meric	Chain A 298–327（30 aa） Chain B 298–327（30 aa） Chain C 298–327（30 aa） Chain D 298–327（30 aa） Chain E 298–327（30 aa） Chain F 298–327（30 aa） Chain G 298–327（30 aa） Chain H 298–327（30 aa） Chain I 298–327（30 aa） Chain J 298–327（30 aa） Chain K 298–327（30 aa） Chain L 298–327（30 aa） Chain M 298–327（30 aa） Chain N 298–327（30 aa） Chain O 298–327（30 aa） Chain P 298–327（30 aa） Chain Q 298–327（30 aa） Chain R 298–327（30 aa） Chain S 298–327（30 aa） Chain T 298–327（30 aa） Chain U 298–327（30 aa） Chain V 298–327（30 aa） Chain W 298–327（30 aa） Chain X 298–327（30 aa） Chain Y 298–327（30 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；In water. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å
9PLL TRIM21-NUP98 Molecular Glue Complex (MAN-056) Deposited 2025-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 712–863（152 aa）	Not recorded	A1BLD (3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000	Resolution 1.60 Å R-free 0.214
9PLM TRIM21-NUP98 Molecular Glue Complex (MAN-021) Deposited 2025-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 712–863（152 aa）	Not recorded	A1CI1 (3P)-3-{4-chloro-2-[2-(dimethylamino)ethoxy]phenyl}-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one × 1 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；100 mM NaCl, 100 mM HEPES, pH 7.5, 12 % polyethylene glycol 20,000	Resolution 1.32 Å R-free 0.178

20 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NUP98_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–187； UniProt 678–863 Author chain C； PDBConstruct 2–187； UniProt 678–863 Author chain B； PDBConstruct 1–57； UniProt 864–920 Author chain D； PDBConstruct 1–57； UniProt 864–920

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ko6
Deposition date deposition_date	2001-12-20
Structure title title	Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98
Keywords keywords	nucleoporin, autoproteolysis, nuclear pore, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.25 Å
Radius of gyration Rg (electron density) rg_electron	21.04 Å
Forward intensity I(0) i0	21133400.00
Molecular weight molecular_weight	35129.0 kDa
Excluded volume excluded_volume	44065 Å³
Envelope volume envelope_volume	52353 Å³
Hydration-shell volume shell_volume	21009 Å³
Envelope diameter envelope_diameter	73.2 Å
Shell Rg shell_rg	27.26 Å
Envelope Rg envelope_rg	21.20 Å
Shape Rg shape_rg	21.00 Å
Total Rg total_rg	22.00 Å
Total atoms total_atoms	2480
Residues n_residues	312
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.1 Å
Rg (real space) rg_real	22.15 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.1130e+07
I(0) uncertainty (real space) i0_real_error	2.3350e+05
Rg (reciprocal space) rg_reciprocal	22.18 Å
I(0) (reciprocal space) i0_reciprocal	21130000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.8 Å
Skewness Skewness skewness	0.148
Kurtosis Kurtosis kurtosis	-0.566
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4457000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Nuclear Pore Complex Protein Nup98
Molecular weight formula_weight	21201.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2480

MAALRNGLEGSSEETSFHDESLQDDREEIENNSYHMHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nuclear Pore Complex Protein Nup98
Molecular weight formula_weight	7111.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SKYGLQDSDEEEEEHPSKTSTKKLKTAPLPPASQTTPLQMALNGKPAPPPQVEKKGQLEHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ko6.1
Class class	b — All beta proteins
Fold Fold fold	b.119 — C-terminal autoproteolytic domain of nucleoporin nup98
Superfamily Superfamily superfamily	b.119.1 — C-terminal autoproteolytic domain of nucleoporin nup98
Family Family family	b.119.1.1 — C-terminal autoproteolytic domain of nucleoporin nup98

Domain ID domain_id	d1ko6.2
Class class	b — All beta proteins
Fold Fold fold	b.119 — C-terminal autoproteolytic domain of nucleoporin nup98
Superfamily Superfamily superfamily	b.119.1 — C-terminal autoproteolytic domain of nucleoporin nup98
Family Family family	b.119.1.1 — C-terminal autoproteolytic domain of nucleoporin nup98

CATH v4.4 (2 domains)

Domain ID domain_id	1ko6A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

Domain ID domain_id	1ko6C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1610 — c-terminal autoproteolytic domain of nucleoporin nup98
Homologous superfamily homologous superfamily	10 — Peptidase S59, nucleoporin

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8. Citations (1)

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Unit-cell length a length_a	89.900 Å
Unit-cell length b length_b	89.900 Å
Unit-cell length c length_c	203.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2470
R_free r_free	0.2710

fit	/app/data/saxs_computation/ko/1ko6/1ko6.fit
pddf	/app/data/pr_computation/ko/1ko6/1ko6.pr.out
profile	/app/data/saxs_computation/ko/1ko6/1ko6.dat

Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98

1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear Pore Complex Protein Nup98

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)