6fga

Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1

Method: X-RAY DIFFRACTION D_max: 194.8 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–98 Chain E； UniProt 1–98	Not recorded	Ubiquitin-conjugating enzyme E2 E1 × 2 （P51965） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–98 Chain C； UniProt 1–98	Not recorded	Ubiquitin-conjugating enzyme E2 E1 × 2 （P51965） 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–98 Chain F； UniProt 1–98	Not recorded	Ubiquitin-conjugating enzyme E2 E1 × 2 （P51965） 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
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 1–98 Chain H； UniProt 1–98	Not recorded	Ubiquitin-conjugating enzyme E2 E1 × 1 （P51965） 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

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 6FGA	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 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 mutation/modification 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 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
6S53 Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate Deposited 2019-06-30	Different construct 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 oligomeric state 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 mutation/modification 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 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 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 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 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 287–463（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 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 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 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 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
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 B 284–465（182 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
9Q9O TRIM21 PRYSPRY bound to compound 36 Deposited 2025-02-26	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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 mutation/modification 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 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 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 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 287–465（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 24 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 A； PDBConstruct 4–101； UniProt 1–98 Author chain B； PDBConstruct 4–101； UniProt 1–98 Author chain C； PDBConstruct 4–101； UniProt 1–98 Author chain D； PDBConstruct 4–101； UniProt 1–98 Author chain E； PDBConstruct 4–101； UniProt 1–98 Author chain F； PDBConstruct 4–101； UniProt 1–98 Author chain G； PDBConstruct 4–101； UniProt 1–98 Author chain H； PDBConstruct 4–101； UniProt 1–98

Ubiquitin-conjugating enzyme E2 E1

Homo sapiens

UniProt P51965

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain K； UniProt 37–193 Chain N； UniProt 37–193	Not recorded	E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain M； UniProt 37–193 Chain O； UniProt 37–193	Not recorded	E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain I； UniProt 37–193 Chain L； UniProt 37–193	Not recorded	E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） 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
4	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain J； UniProt 37–193	Not recorded	E3 ubiquitin-protein ligase TRIM21 × 2 （P19474） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6FGA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XR9 Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3 Deposited 2004-10-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 83–91（9 aa） Fragment：residues 83-91	Not recorded	SO4 SULFATE ION × 2 URE UREA × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.2M NH4Ac, 0.1M tri-Sodium Citrate dihydrate, pH 5.6, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.79 Å R-free 0.232
3BZH Crystal structure of human ubiquitin-conjugating enzyme E2 E1 Deposited 2008-01-18	Different construct 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 1–193（193 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；2.2M (NH4)2SO4, 0.1M Bis-Tris-Propane pH 9.0, 0.001M DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.60 Å R-free 0.226
4JJQ Crystal structure of usp7-ntd with an e2 enzyme Deposited 2013-03-08	Different construct 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 5–14（10 aa） Fragment：UNP RESIDUES 5-14	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30 % PEG 4000, 0.1 M TRIS PH 8.5 AND 0.2 M LITHIUM SULFATE , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.95 Å R-free 0.217
5LBN High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6 Deposited 2016-06-16	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 37–193（157 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M Sodium citrate pH 6 and 8% (w/v) PEG 8000	Resolution 1.42 Å R-free 0.183
8IYA Complex of SETDB1-derived peptide bound to UBE2E1 Deposited 2023-04-04	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 41–193（153 aa）	Mutation：C67S, C122P, C153S, C159P	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium sulfate, 0.1 M MES pH6.5	Resolution 2.43 Å R-free 0.247
8IYA Complex of SETDB1-derived peptide bound to UBE2E1 Deposited 2023-04-04	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 A 41–193（153 aa）	Mutation：C67S, C122P, C153S, C159P	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium sulfate, 0.1 M MES pH6.5	Resolution 2.43 Å R-free 0.247
8IYA Complex of SETDB1-derived peptide bound to UBE2E1 Deposited 2023-04-04	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 C 41–193（153 aa）	Mutation：C67S, C122P, C153S, C159P	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Lithium sulfate, 0.1 M MES pH6.5	Resolution 2.43 Å R-free 0.247

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UB2E1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 2–158； UniProt 37–193 Author chain J； PDBConstruct 2–158； UniProt 37–193 Author chain K； PDBConstruct 2–158； UniProt 37–193 Author chain L； PDBConstruct 2–158； UniProt 37–193 Author chain M； PDBConstruct 2–158； UniProt 37–193 Author chain N； PDBConstruct 2–158； UniProt 37–193 Author chain O； PDBConstruct 2–158； UniProt 37–193

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	6fga
Deposition date deposition_date	2018-01-10
Structure title title	Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1
Keywords keywords	RING-type E3 ligase, UBC core domain and Ubiquitination, 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	50.98 Å
Radius of gyration Rg (electron density) rg_electron	51.49 Å
Forward intensity I(0) i0	536665000.00
Molecular weight molecular_weight	188180.0 kDa
Excluded volume excluded_volume	234480 Å³
Envelope volume envelope_volume	362210 Å³
Hydration-shell volume shell_volume	63331 Å³
Envelope diameter envelope_diameter	209.9 Å
Shell Rg shell_rg	49.37 Å
Envelope Rg envelope_rg	51.14 Å
Shape Rg shape_rg	51.57 Å
Total Rg total_rg	51.12 Å
Total atoms total_atoms	13097
Residues n_residues	1667
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	194.8 Å
Rg (real space) rg_real	51.38 Å
Rg uncertainty (real space) rg_real_error	2.60 Å
I(0) (real space) i0_real	5.3670e+08
I(0) uncertainty (real space) i0_real_error	1.0780e+07
Rg (reciprocal space) rg_reciprocal	50.66 Å
I(0) (reciprocal space) i0_reciprocal	536200000.0000
Solution quality estimate total_estimate	0.8021
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	56.6 Å
Skewness Skewness skewness	0.686
Kurtosis Kurtosis kurtosis	0.450
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25640000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.577; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.889

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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	11176.9 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	13206

GSHMASAARLTMMWEEVTCPICLDPFVEPVSIECGHSFCQECISQVGKGGGSVCPVCRQRFLLKNLRPNRQLANMVNNLKEISQEAREGTQGERCAVHGER

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 BL21

Entity 2 Entity 2 polymer

Description description	Ubiquitin-conjugating enzyme E2 E1
Molecular weight formula_weight	17619.2 kDa
EC 编号 ec_number	2.3.2.23,2.3.2.24
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O

GSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT

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 BL21

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	16

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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	109

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7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d6fgai_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgaj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgak_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgal_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgam_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgan_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6fgao_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

CATH v4.4 (15 domains)

Domain ID domain_id	6fgaA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	6fgaI00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaJ00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaL00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaM00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaN00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6fgaO00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	103.835 Å
Unit-cell length b length_b	95.871 Å
Unit-cell length c length_c	235.097 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.820 Å
Low-resolution limit resolution_low	47.900 Å
R factor r_factor	0.2549
R_work r_work	0.2528
R_free r_free	0.2941

fit	/app/data/saxs_computation/fg/6fga/6fga.fit
pddf	/app/data/pr_computation/fg/6fga/6fga.pr.out
profile	/app/data/saxs_computation/fg/6fga/6fga.dat

Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1

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

Ubiquitin-conjugating enzyme E2 E1

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

7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (7 domains)

CATH v4.4 (15 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)