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2oni

Catalytic Domain of the Human NEDD4-like E3 Ligase

Method: X-RAY DIFFRACTION Dmax: 79.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 ubiquitin-protein ligase NEDD4-like protein

Homo sapiens

UniProt Q96PU5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 594–967 Fragment：Hect Domain (ubiquitin transferase) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947. Resolution 2.20 Å R-free 0.259
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 594–967 Fragment：Hect Domain (ubiquitin transferase) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947. Resolution 2.20 Å R-free 0.259
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 594–967 Fragment：Hect Domain (ubiquitin transferase) Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；THE PROTEIN WAS DISSOLVED AT 10 mg/mL IN 10 mM TRIS-HCL, PH 8.0, 100 mM NaCl, 2% GLYCEROL AND 1 mM DTT. CRYSTALS WERE GROWN BY VAPOR DIFFUSION, HANGING DROPS BY MIXING 2 MICROL PROTEIN SOLUTION WITH 2 MICROL WELL SOLUTION (1.7 M SODIUM/POTASSIUM PHOSPHATE, PH 6.0, 1 mM DTT) AT TEMPERATURE 294.0K. FOR CRYOPROTECTION, THE CRYSTALS WERE SOAKED IN 2 M SODIUM-POTASSIUM PHOSPHATE, pH 7.0, 1 mM DTT, 25% ETHYLENE GLYCOL AND 2 mG/mL SEMETNEDD4L.574.947. Resolution 2.20 Å R-free 0.259

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 2ONI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LAJ Third WW domain of human Nedd4L in complex with doubly phosphorylated human smad3 derived peptide Deposited 2011-03-16 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 A 496–535（40 aa） Fragment：WW 3 domain residues 496-535
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient
NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LB2 Structure of the second domain of human Nedd4L in complex with a phosphorylated pTPY motif derived from human Smad3 Deposited 2011-03-22 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 × 2 PDB declaration: dimeric
Chain A 386–420（35 aa） Fragment：residues 386-420
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；285 K；Ionic strength (raw mmCIF value) 0.420；Pressure ambient
NMR sample composition 1 mM NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW3, 3 mM SMAD3, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LTY NEDD4L WW2 domain in complex with a Smad7 derived peptide Deposited 2012-06-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 385–417（33 aa） Fragment：WW2 domain (UNP residues 385-417)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；285 K；Pressure ambient
NMR sample composition 1 mM NEDD4LWW2, 2 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] NEDD4LWW2, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MPT WW3 domain of Nedd4L in complex with its HECT domain PY motif Deposited 2014-06-02 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 496–539（44 aa） Fragment：WW3 domain, UNP RESIDUES 496-539
Chain B 945–957（13 aa） Fragment：HECT domain PY motif, UNP RESIDUES 945-957
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Pressure ambient
NMR sample composition 0.7 mM WW3-1, 1.4 mM HECT_PY-2, 150 mM sodium chloride-3, 20 mM sodium phosphate-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] WW3-5, 2 mM HECT_PY-6, 150 mM sodium chloride-7, 20 mM sodium phosphate-8, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] WW3-9, 1.6 mM HECT_PY-10, 150 mM sodium chloride-11, 20 mM sodium phosphate-12, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NSQ Crystal structure of the C2 domain of the human E3 ubiquitin-protein ligase NEDD4-like protein Deposited 2006-11-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–154（154 aa） Fragment：C2 Domain
Not recorded EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；298 K；14% PEG 4000, 0.2 M NaOAc, pH 6.5, 1 mM DTT. 20% Ethylene glycol added as cryoprotectant, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.50
Resolution 1.85 Å R-free 0.218
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 596–975（380 aa） Fragment：HECT domain
Mutation：576-949, C922A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.267
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17 Different construct Different mutation/modification 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 596–975（380 aa） Fragment：HECT domain
Mutation：576-949, C922A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, pH 5.1-5.2, 2.4-2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.30 Å R-free 0.267
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 596–975（380 aa） Fragment：NEDD4L HECT DOMAIN (UNP 576-955)
Mutation：UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
3JW0 E2~Ubiquitin-HECT Deposited 2009-09-17 Different construct Different mutation/modification 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 596–975（380 aa） Fragment：NEDD4L HECT DOMAIN (UNP 576-955)
Mutation：UBIQUITIN G76 ESTER-LINKED TO UBCH5B TO S85 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；277 K；0.1 M sodium citrate, 2.4M sodium chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.287
5HPK System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: NEDD4L and UbV NL.1 Deposited 2016-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 594–975（382 aa） Fragment：HECT domain (UNP residues 594-975)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Sodium cacodylate, NaCl, PEG 8000, 1-butanol
Resolution 2.43 Å R-free 0.227
6ZBT Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342 Deposited 2020-06-09 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 E 338–347（10 aa）
Chain G 338–347（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.80 Å R-free 0.241
6ZBT Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser342 Deposited 2020-06-09 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 F 338–347（10 aa）
Chain H 338–347（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.80 Å R-free 0.241
6ZC9 Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448 Deposited 2020-06-10 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 E 444–453（10 aa）
Chain G 444–453（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.90 Å R-free 0.239
6ZC9 Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448 Deposited 2020-06-10 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 F 444–453（10 aa）
Chain H 444–453（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) CFH 1,1,1,3,3,3-hexafluoropropan-2-ol × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；PEG 400, magnesium chloride, HEPES, hexafluoro-2-propanol
Resolution 1.90 Å R-free 0.239
7LP1 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 494–532（39 aa） Fragment：WW 3 domain, residues 494-532
Not recorded NO3 NITRATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293.15 K；3.6M ammonium nitrate, 5% glycerol, and 0.1M sodium acetate at pH 4.6
Resolution 1.35 Å R-free 0.213
7LP3 Structure of Nedd4L WW3 domain Deposited 2021-02-11 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 A 193–226（34 aa） Fragment：WW 1 domain, residues 193-226
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate
Resolution 1.61 Å R-free 0.210
7LP3 Structure of Nedd4L WW3 domain Deposited 2021-02-11 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 C 193–226（34 aa） Fragment：WW 1 domain, residues 193-226
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；310 K；1.6M (NH4)2SO4, 0.1M Potassium Sodium Tartrate, 5% glycerol, 0.1M Sodium Acetate
Resolution 1.61 Å R-free 0.210
7LP4 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Different construct Different mutation/modification 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 493–539（47 aa） Fragment：WW 3 domain, residues 493-539
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] E3 ubiquitin-protein ligase NEDD4-like, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7LP5 Structure of Nedd4L WW3 domain Deposited 2021-02-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 493–539（47 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Angiomotin,E3 ubiquitin-protein ligase NEDD4-like fusion, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 15N] Angiomotin,E3 ubiquitin-protein ligase NEDD4-like fusion, 20 mM sodium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
7NMZ Structure of 14-3-3 eta in complex with Nedd4-2(335-455) containing two 14-3-3 binding motifs Ser342 and Ser448 Deposited 2021-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 335–455（121 aa）
Mutation：T367A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M of each NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1Mbicine/Trizma base pH 8.5, 30% sacharose
Resolution 2.30 Å R-free 0.235
9GIK Full-lenght Nedd4-2 E3 ubiquitin ligase Deposited 2024-08-19 Different construct Different mutation/modification 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 1–955（955 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 130 mM KCl, 20 mM NaCl, 1 mM EDTA, 1 mM TCEP, 3mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9GIM Full-lenght Nedd4-2 E3 ubiquitin ligase in presence of Ca2+ Deposited 2024-08-19 Different construct Different mutation/modification 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 1–955（955 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 130 mM KCl, 20 mM NaCl, 1 mM TCEP, 1mM CaCl2, 3mM CHAPSO
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.11 Å
9Z5Q HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11 Deposited 2025-11-12 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 541–975（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 150 mM NaCl, 1 mM TCEP, and 1 mM EDTA, 0.043% CHAPS
cryo-EM vitrification conditions Cryogen ETHANE；Vitrification carried out at Argon atmosphere
Resolution 3.06 Å

18 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NED4L_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 19–392； UniProt 594–967

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 2oni

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2oni
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2oni
Deposition date deposition_date2007-01-24
Structure title titleCatalytic Domain of the Human NEDD4-like E3 Ligase
Keywords keywordsALPHA and BETA PROTEIN (a + b), E3 LIGASE, HECT DOMAIN, UBL-CONJUGATION PATHWAY, STRUCTURAL GENOMICS CONSORTIUM, SGC, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.92 Å
Radius of gyration Rg (electron density) rg_electron23.87 Å
Forward intensity I(0) i033707100.00
Molecular weight molecular_weight44820.0 kDa
Excluded volume excluded_volume55890 ų
Envelope volume envelope_volume68388 ų
Hydration-shell volume shell_volume24583 ų
Envelope diameter envelope_diameter80.0 Å
Shell Rg shell_rg30.27 Å
Envelope Rg envelope_rg23.78 Å
Shape Rg shape_rg23.88 Å
Total Rg total_rg24.64 Å
Total atoms total_atoms3122
Residues n_residues364
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 dmax79.2 Å
Rg (real space) rg_real24.82 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real3.3710e+07
I(0) uncertainty (real space) i0_real_error4.8980e+05
Rg (reciprocal space) rg_reciprocal24.85 Å
I(0) (reciprocal space) i0_reciprocal33710000.0000
Solution quality estimate total_estimate0.9059
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.4 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.613
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8272000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2onia1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.148 — Hect, E3 ligase catalytic domain
Superfamily Superfamily superfamilyd.148.1 — Hect, E3 ligase catalytic domain
Family Family familyd.148.1.0 — automated matches
Domain ID domain_idd2onia2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id2oniA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1750 — Hect, E3 ligase catalytic domain fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domains
Domain ID domain_id2oniA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2160 — Hect, E3 ligase catalytic domain
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
Domain ID domain_id2oniA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2410 — Hect, E3 ligase catalytic fold
Homologous superfamily homologous superfamily10 — Hect, E3 ligase catalytic domain
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8. Citations (1)

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9. Files and Curves (10)