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7q67

Cryo-em structure of the Nup98 fibril polymorph 4

Method: ELECTRON MICROSCOPY Dmax: 80.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nuclear pore complex protein Nup98

Homo sapiens

UniProt P52948

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 × 11 PDB declaration: undecameric（11） Consistent with protein copy count Chain A； UniProt 85–124 Chain B； UniProt 85–124 Chain C； UniProt 85–124 Chain D； UniProt 85–124 Chain E； UniProt 85–124 Chain F； UniProt 85–124 Chain G； UniProt 85–124 Chain H； UniProt 85–124 Chain I； UniProt 85–124 Chain J； UniProt 85–124 Chain K； UniProt 85–124 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.37 Å

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 7Q67 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1KO6 Crystal Structure of C-terminal Autoproteolytic Domain of Nucleoporin Nup98 Deposited 2001-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 678–863（186 aa） Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 677-863)
Chain B 864–920（57 aa） Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 864-920)
Chain C 678–863（186 aa） Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 677-863)
Chain D 864–920（57 aa） Fragment：C-terminal Autoproteolytic Domain (Sequence database residues 864-920)
Not recorded No recorded non-water small molecule 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
2Q5X Crystal Structure of the C-terminal domain of hNup98 Deposited 2007-06-03 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 mutation/modification Different oligomeric state 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 method 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 method 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 method 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 method 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 mutation/modification Different oligomeric state 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 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 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 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
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10 Different construct Different oligomeric state 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 oligomeric state 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 method 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 method 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
Chains and sequence ranges Author chain A； PDBConstruct 1–40； UniProt 85–124 Author chain B； PDBConstruct 1–40； UniProt 85–124 Author chain C； PDBConstruct 1–40； UniProt 85–124 Author chain D； PDBConstruct 1–40； UniProt 85–124 Author chain E； PDBConstruct 1–40； UniProt 85–124 Author chain F； PDBConstruct 1–40； UniProt 85–124 Author chain G； PDBConstruct 1–40； UniProt 85–124 Author chain H； PDBConstruct 1–40； UniProt 85–124 Author chain I； PDBConstruct 1–40； UniProt 85–124 Author chain J； PDBConstruct 1–40； UniProt 85–124 Author chain K； PDBConstruct 1–40； UniProt 85–124

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

SAXS profile for 7q67

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7q67
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7q67
Deposition date deposition_date2021-11-05
Structure title titleCryo-em structure of the Nup98 fibril polymorph 4
Keywords keywordsNuclear pore complex protein Nup98 functional amyloid fibril PROTEIN FIBRIL, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.06 Å
Radius of gyration Rg (electron density) rg_electron22.01 Å
Forward intensity I(0) i024972700.00
Molecular weight molecular_weight36912.0 kDa
Excluded volume excluded_volume45476 ų
Envelope volume envelope_volume51927 ų
Hydration-shell volume shell_volume20813 ų
Envelope diameter envelope_diameter82.1 Å
Shell Rg shell_rg27.97 Å
Envelope Rg envelope_rg22.40 Å
Shape Rg shape_rg21.94 Å
Total Rg total_rg22.94 Å
Total atoms total_atoms2618
Residues n_residues363
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax80.5 Å
Rg (real space) rg_real22.19 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real2.4970e+07
I(0) uncertainty (real space) i0_real_error3.8140e+05
Rg (reciprocal space) rg_reciprocal22.17 Å
I(0) (reciprocal space) i0_reciprocal24970000.0000
Solution quality estimate total_estimate0.8207
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.8 Å
Skewness Skewness skewness0.501
Kurtosis Kurtosis kurtosis-0.198
Angular range angular_range— – 0.3600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3761000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.694; Smooth: 0.975
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)