SAXSdb — 9z5q

▼

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

E3 ubiquitin-protein ligase NEDD4-like

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 541–975	Not recorded	Nanobody C11 (nb.C11) × 1	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

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 9Z5Q	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 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 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 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 oligomeric state 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 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 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
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24	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 × 2 PDB declaration: dimeric	Chain A 594–967（374 aa） 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
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 594–967（374 aa） 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
2ONI Catalytic Domain of the Human NEDD4-like E3 Ligase Deposited 2007-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 594–967（374 aa） 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
3JVZ E2~Ubiquitin-HECT Deposited 2009-09-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 method 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 experimental method 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 method 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 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state 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 oligomeric state 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 experimental method 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 oligomeric state 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 oligomeric state 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

18 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NED4L_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–437； UniProt 541–975

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z5q
Deposition date deposition_date	2025-11-12
Structure title title	HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11
Keywords keywords	Ubiquitin, targeted protein degradation, E3 ligase, Nanobody, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	27.83 Å
Radius of gyration Rg (electron density) rg_electron	26.75 Å
Forward intensity I(0) i0	62913900.00
Molecular weight molecular_weight	62719.0 kDa
Excluded volume excluded_volume	78694 Å³
Envelope volume envelope_volume	96485 Å³
Hydration-shell volume shell_volume	30344 Å³
Envelope diameter envelope_diameter	95.5 Å
Shell Rg shell_rg	33.69 Å
Envelope Rg envelope_rg	26.58 Å
Shape Rg shape_rg	26.75 Å
Total Rg total_rg	27.51 Å
Total atoms total_atoms	8716
Residues n_residues	539
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

▼

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

Maximum dimension Dmax dmax	88.8 Å
Rg (real space) rg_real	27.71 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	6.2910e+07
I(0) uncertainty (real space) i0_real_error	9.0130e+05
Rg (reciprocal space) rg_reciprocal	27.75 Å
I(0) (reciprocal space) i0_reciprocal	62920000.0000
Solution quality estimate total_estimate	0.9061
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15100000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Nanobody C11 (nb.C11)
Molecular weight formula_weight	17817.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8716

MKYLLPTAAAGLLLLAAQPAMAMDIGINSDPQVQLQESGGGLVQAGGSLRLSCAASGNISDVWYMGWYRQAPGKEREFVAGIAYGTSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVIITRFVSYPRQHTYWGQGTQVTVSSPLEHHHHHH

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	E3 ubiquitin-protein ligase NEDD4-like
Molecular weight formula_weight	52598.5 kDa
EC 编号 ec_number	2.3.2.26,2.3.2.36
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SYSLNPNDLGPLPPGWEERIHLDGRTFYIDHNSKITQWEDPRLQNPAITGPAVPYSREFKQKYDYFRKKLKKPADIPNRFEMKLHRNNIFEESYRRIMSVKRPDVLKARLWIEFESEKGLDYGGVAREWFFLLSKEMFNPYYGLFEYSATDNYTLQINPNSGLCNEDHLSYFTFIGRVAGLAVFHGKLLDGFFIRPFYKMMLGKQITLNDMESVDSEYYNSLKWILENDPTELDLMFCIDEENFGQTYQVDLKPNGSEIMVTNENKREYIDLVIQWRFVNRVQKQMNAFLEGFTELLPIDLIKIFDENELELLMCGLGDVDVNDWRQHSIYKNGYCPNHPVIQWFWKAVLLMDAEKRIRLLQFVTGTSRVPMNGFAELYGSNGPQLFTIEQWGSPEKLPRAHTCFNRLDLPPYETFEDLREKLLMAVENAQGFEGVDMDYKDDDDK

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(DE3)

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.060 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.06 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	90979

fit	/app/data/saxs_computation/z5/9z5q/9z5q.fit
pddf	/app/data/pr_computation/z5/9z5q/9z5q.pr.out
profile	/app/data/saxs_computation/z5/9z5q/9z5q.dat

HECT domain of NEDD4-2 complex with a targeted nanobody, nb.C11

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

E3 ubiquitin-protein ligase NEDD4-like

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)