9plm

TRIM21-NUP98 Molecular Glue Complex (MAN-021)

Method: X-RAY DIFFRACTION D_max: 76.9 Å Quality: GOOD

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

E3 ubiquitin-protein ligase TRIM21

Homo sapiens

UniProt P19474

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 284–465	Not recorded	Isoform 2 of Nuclear pore complex protein Nup98-Nup96 × 1 （P52948） 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

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 9PLM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IWG COMPLEX BETWEEN THE PRYSPRY DOMAIN OF TRIM21 AND IGG FC Deposited 2006-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 287–465（179 aa） Fragment：RESIDUES 287-465 Chain E 287–465（179 aa） Fragment：RESIDUES 287-465	Not recorded	FUC alpha-L-fucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.35 Å R-free 0.253
5JPX Solution structure of the TRIM21 B-box2 (B2) Deposited 2016-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–130（45 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50mM TRIS, 150mM NaCl；Pressure Ambient NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50mM TRIS, 150mM NaCl；Pressure Ambient NMR sample composition 450 uM [U-13C; U-15N] TRIM21 Bbox2, 50 mM TRIS, 150 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM ZINC ION, 10 % glycerol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 450 uM [U-13C; U-15N] TRIM21 Bbox2, 50 mM deuterated TRIS, 150 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM ZINC ION, 10 % glycerol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5OLM TRIM21 Deposited 2017-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–129（129 aa） Chain B 1–129（129 aa）	Not recorded	ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；300 K；na	Resolution 1.95 Å R-free 0.262
6FGA Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1 Deposited 2018-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–98（98 aa） Chain E 1–98（98 aa）	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM Bicine pH 9.0 and 5% w/v PEG 6000	Resolution 2.82 Å R-free 0.294
6FGA Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1 Deposited 2018-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–98（98 aa） Chain C 1–98（98 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM Bicine pH 9.0 and 5% w/v PEG 6000	Resolution 2.82 Å R-free 0.294
6FGA Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1 Deposited 2018-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–98（98 aa） Chain F 1–98（98 aa）	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM Bicine pH 9.0 and 5% w/v PEG 6000	Resolution 2.82 Å R-free 0.294
6FGA Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1 Deposited 2018-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–98（98 aa） Chain H 1–98（98 aa）	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100mM Bicine pH 9.0 and 5% w/v PEG 6000	Resolution 2.82 Å R-free 0.294
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–85（85 aa） Chain B 1–85（85 aa）	Not recorded	ZN ZINC ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.	Resolution 2.80 Å R-free 0.249
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 1–85（85 aa） Chain H 1–85（85 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.	Resolution 2.80 Å R-free 0.249
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–85（85 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K	Resolution 2.20 Å R-free 0.252
8A58 X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–85（85 aa） Chain D 1–85（85 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；0.1 M Bicine pH 9.0, 5% PEG 6000, 0.1M TCEP hydrochloride	Resolution 2.25 Å R-free 0.259
8Y58 Crystal structure of TRIM21 PRYSPRY (D355A) in complex with acepromazine. Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–475（189 aa）	Mutation：D355A	PMZ 1-[10-(3-DIMETHYLAMINO-PROPYL)-10H-PHENOTHIAZIN-2-YL]-ETHANONE × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Tris (pH 7.0), 3.5 M sodium formate	Resolution 1.60 Å R-free 0.203
8Y59 Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (S)-hydroxyl-acepromazine. Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–475（189 aa）	Mutation：D355A	A1D5Y (1~{S})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Tris (pH 7.0), 3.5 M sodium formate	Resolution 1.89 Å R-free 0.234
8Y5B Crystal structure of TRIM21 PRYSPRY (D355A) in complex with (R)-hydroxyl-acepromazine. Deposited 2024-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–475（189 aa）	Mutation：D355A	A1D5Z (1~{R})-1-[10-[3-(dimethylamino)propyl]phenothiazin-2-yl]ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Tris (pH 7.0), 3.5 M sodium formate	Resolution 1.74 Å R-free 0.203
9EK5 TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog Deposited 2024-11-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 288–465（178 aa） Fragment：PrySpry domain	Not recorded	A1BLD (3P)-3-(4-chloro-2-ethoxyphenyl)-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；4.2 M Sodium Formate; 100 mM Tris-HCl, pH 7.5	Resolution 2.10 Å R-free 0.265
9II5 Crystal structure of human TRIM21 PRYSPRY in complex with compound 1 Deposited 2024-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–463（177 aa）	Not recorded	A1D9F ~{N}-[(1-fluoranylcyclohexyl)methyl]-~{N}-methyl-4-(2-methylsulfanylphenyl)-2-methylsulfonyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；291 K；1. Cryo buffer: 80 uL TRIM21 (Reservoir Solution: 0.1 M Cirtic, pH 3.5, 3 M NaCl) + 20 uL glycerol 2. Soaked crystals in cryo buffer for 10s	Resolution 1.49 Å R-free 0.240
9M3N Crystal structure of human TRIM21 PRYSPRY in complex with T-02 Deposited 2025-03-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 285–464（180 aa）	Not recorded	A1EMT 1-ethyl-~{N}-methyl-5-phenyl-~{N}-[3-[3-(trifluoromethyl)phenyl]cyclobutyl]pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；The solution contained 0.1 M BIS-TRIS propane (pH 7.0) and 1.2 M potassium sodium tartrate tetrahydrate.	Resolution 2.08 Å R-free 0.235
9PLL TRIM21-NUP98 Molecular Glue Complex (MAN-056) Deposited 2025-07-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 284–465（182 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
9Q9O TRIM21 PRYSPRY bound to compound 36 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 287–475（189 aa）	Not recorded	A1I4Z 4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate	Resolution 2.46 Å R-free 0.368
9Q9O TRIM21 PRYSPRY bound to compound 36 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–475（189 aa）	Not recorded	A1I4Z 4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate	Resolution 2.46 Å R-free 0.368
9Q9O TRIM21 PRYSPRY bound to compound 36 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 287–475（189 aa）	Not recorded	A1I4Z 4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate	Resolution 2.46 Å R-free 0.368
9Q9O TRIM21 PRYSPRY bound to compound 36 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 287–475（189 aa）	Not recorded	A1I4Z 4-[[[4-imidazol-1-yl-3-[1-[(4-methoxyphenyl)methyl]-3-methyl-pyrazol-4-yl]phenyl]methylamino]methyl]-~{N}-methyl-benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20% PEG 4000, 5% iso-Propanol, 0.1 M Na Citrate	Resolution 2.46 Å R-free 0.368
9Q9P TRIM21 PRYSPRY bound to compound 37 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 287–475（189 aa）	Not recorded	A1I4X (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(2-methoxyphenyl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；30% PEG 10000, 0.1 M TRIS HCl pH 8.5	Resolution 2.10 Å R-free 0.296
9Q9Q TRIM21 PRYSPRY bound to compound 38 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 287–475（189 aa）	Not recorded	A1I4Y (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(furan-2-yl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；30% PEG 10000, 0.1 M TRIS HCl pH 8.5	Resolution 2.25 Å R-free 0.325
9Q9Q TRIM21 PRYSPRY bound to compound 38 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–475（189 aa）	Not recorded	A1I4Y (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-(furan-2-yl)propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；30% PEG 10000, 0.1 M TRIS HCl pH 8.5	Resolution 2.25 Å R-free 0.325
9Q9R TRIM21 PRYSPRY bound to compound 209 Deposited 2025-02-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 287–475（189 aa）	Not recorded	A1I4W (2~{S},4~{S})-1-[(3~{S})-3-azanyl-3-[2-[2-(2-hydroxyethyloxy)ethoxy]phenyl]propanoyl]-4-cyclohexyl-~{N}-[(2~{S})-1-(methylamino)-1-oxidanylidene-3-pyridin-4-yl-propan-2-yl]pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.6；291.15 K；20% (w/v) PEG-8000, 0.1M CHES pH 9.5 (final pH 9.6)	Resolution 2.33 Å R-free 0.314
9QBA Human TRIM21 PRYSPRY domain in complex with AL236 Deposited 2025-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 287–465（179 aa）	Not recorded	A1I41 ~{N}-(cyclohexylmethyl)-4-(4-fluoranyl-2-methylsulfanyl-phenyl)-2-methylsulfonyl-benzamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；298 K；2.3 M Sodium Chloride 0.1 M Sodium Citrate	Resolution 1.45 Å R-free 0.162

19 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RO52_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 3–184； UniProt 284–465

Isoform 2 of Nuclear pore complex protein Nup98-Nup96

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 712–863	Not recorded	E3 ubiquitin-protein ligase TRIM21 × 1 （P19474） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9PLM	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 ligand/ion 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

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	P52948-2
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 20–171； UniProt 712–863

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	9plm
Deposition date deposition_date	2025-07-15
最后修订 last_revision	2026-05-27
Structure title title	TRIM21-NUP98 Molecular Glue Complex (MAN-021)
Keywords keywords	molecular glue, ubiquitin ligase, TRIM21, targeted protein degradation, LIGASE; LIGASE
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	23.16 Å
Radius of gyration Rg (electron density) rg_electron	22.29 Å
Forward intensity I(0) i0	47910200.00
Molecular weight molecular_weight	36125.0 kDa
Excluded volume excluded_volume	34998 Å³
Envelope volume envelope_volume	57857 Å³
Hydration-shell volume shell_volume	22079 Å³
Envelope diameter envelope_diameter	82.5 Å
Shell Rg shell_rg	28.63 Å
Envelope Rg envelope_rg	22.54 Å
Shape Rg shape_rg	22.25 Å
Total Rg total_rg	22.94 Å
Total atoms total_atoms	2739
Residues n_residues	335
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	76.9 Å
Rg (real space) rg_real	23.16 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	4.7910e+07
I(0) uncertainty (real space) i0_real_error	6.6160e+05
Rg (reciprocal space) rg_reciprocal	23.17 Å
I(0) (reciprocal space) i0_reciprocal	47910000.0000
Solution quality estimate total_estimate	0.8097
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.336
Kurtosis Kurtosis kurtosis	-0.409
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6250000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase TRIM21
Molecular weight formula_weight	20736.2 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	3202

SGTSAVHITLDPDTANPWLILSEDRRQVRLGDTQQSIPGNEERFDSYPMVLGAQHFHSGKHYWEVDVTGKEAWDLGVCRDSVRRKGHFLLSSKSGFWTIWLWNKQKYEAGTYPQTPLHLQVPPCQVGIFLDYEAGMVSFYNITDHGSLIYSFSECAFTGPLRPFFSPGFNDGGKNTAPLTLCPL

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	Isoform 2 of Nuclear pore complex protein Nup98-Nup96
Molecular weight formula_weight	19535.0 kDa
EC 编号 ec_number	3.4.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKSSHHHHHHENLYFQSNAMHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF

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 3 Entity 3 non-polymer

Description description	(3P)-3-{4-chloro-2-[2-(dimethylamino)ethoxy]phenyl}-6-fluoro-2-[(piperazin-1-yl)methyl]quinazolin-4(3H)-one
Molecular weight formula_weight	459.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	463

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8. Citations (1)

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Unit-cell length a length_a	56.978 Å
Unit-cell length b length_b	71.495 Å
Unit-cell length c length_c	97.195 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.320 Å
Low-resolution limit resolution_low	49.180 Å
R factor r_factor	—
R_work r_work	0.1503
R_free r_free	0.1781

fit	/app/data/saxs_computation/pl/9plm/9plm.fit
pddf	/app/data/pr_computation/pl/9plm/9plm.pr.out
profile	/app/data/saxs_computation/pl/9plm/9plm.dat

TRIM21-NUP98 Molecular Glue Complex (MAN-021)

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

E3 ubiquitin-protein ligase TRIM21

State in the Current Structure

Other States of the Same Protein in the Database

Isoform 2 of Nuclear pore complex protein Nup98-Nup96

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)