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1zvd

Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT domain

Method: X-RAY DIFFRACTION Dmax: 84.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Smad ubiquitination regulatory factor 2

Homo sapiens

UniProt Q9HAU4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 369–748 Fragment：HECT Domain Non-standard monomer：Yes (specific site not provided by mmCIF) NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；Sodium Phosphate, Potassium Phosphate, and Sodium Acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.248

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 1ZVD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DJY Solution structure of Smurf2 WW3 domain-Smad7 PY peptide complex Deposited 2006-04-06 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 297–333（37 aa） Fragment：WW3 domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Pressure 1
Resolution not provided
2JQZ Solution Structure of the C2 domain of human Smurf2 Deposited 2007-06-15 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 10–140（131 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient
NMR sample composition 20 mM HEPES, 200 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM hepes, 200 mM sodium chloride, 3 mM DTT, 0.03 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
2KXQ Solution Structure of Smurf2 WW2 and WW3 bound to Smad7 PY motif containing peptide Deposited 2010-05-11 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 × 2 PDB declaration: dimeric
Chain A 250–333（84 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 235；Pressure ambient
NMR sample composition 1.2 mM [U-100% 13C; U-100% 15N] WW23, 1.2 mM [U-100% 13C; U-100% 15N] S7PY, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LTZ Smurf2 WW3 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 297–333（37 aa） Fragment：WW3 domain (UNP residues 297-333)
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 SMURF2WW3, 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] SMURF2WW3, 3 mM SMAD7, 20 mM [U-100% 2H] TRIS, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 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 631–745（115 aa）
Mutation：C646A, C706N, C743S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
6FX4 Disulfide between E3 HECT ligase Smurf2 and Ubiquitin G76C Deposited 2018-03-08 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 631–745（115 aa）
Mutation：C646A, C706N, C743S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；1.36M tri-Sodium citrat pH6.5, 15% (v/v) Glycerol
Resolution 2.50 Å R-free 0.239
7M3Q Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV) Deposited 2021-03-18 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 366–748（383 aa）
Not recorded SO4 SULFATE ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 6 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.5 M Ammonium Sulphate and 100 mM MES pH 6.0. Trypsin was added to the protein complex at a final concentration of 10 microgram per mL
Resolution 2.50 Å R-free 0.235
9FSH Crystal structure of the HECT domain of Smurf 2 in complex with inhibitor 8 Deposited 2024-06-21 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 251–748（498 aa）
Not recorded TJQ ethyl 5-[1,3-benzodioxol-5-ylmethyl(ethyl)carbamoyl]-2,4-dimethyl-1~{H}-pyrrole-3-carboxylate × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M NaH2PO4/K2HPO4 pH 6.8, 100 mM NaOAc
Resolution 2.08 Å R-free 0.259

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMUF2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–380； UniProt 369–748

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 1zvd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zvd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zvd
Deposition date deposition_date2005-06-01
Structure title titleRegulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT domain
Keywords keywordsUbiquitin LigaseCatalytic Mechanism, x-ray crystal structure, TGFbeta, 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_guinier24.99 Å
Radius of gyration Rg (electron density) rg_electron23.99 Å
Forward intensity I(0) i032493300.00
Molecular weight molecular_weight44170.0 kDa
Excluded volume excluded_volume55329 ų
Envelope volume envelope_volume67701 ų
Hydration-shell volume shell_volume24453 ų
Envelope diameter envelope_diameter83.8 Å
Shell Rg shell_rg30.26 Å
Envelope Rg envelope_rg24.19 Å
Shape Rg shape_rg23.99 Å
Total Rg total_rg24.76 Å
Total atoms total_atoms3095
Residues n_residues366
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 dmax84.0 Å
Rg (real space) rg_real24.99 Å
Rg uncertainty (real space) rg_real_error0.74 Å
I(0) (real space) i0_real3.2490e+07
I(0) uncertainty (real space) i0_real_error4.1650e+05
Rg (reciprocal space) rg_reciprocal24.99 Å
I(0) (reciprocal space) i0_reciprocal32490000.0000
Solution quality estimate total_estimate0.8010
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary76.0 Å
Skewness Skewness skewness0.321
Kurtosis Kurtosis kurtosis-0.417
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8305000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 0.990; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1zvda_
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

CATH v4.4 (3 domains)

Domain ID domain_id1zvdA01
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_id1zvdA02
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_id1zvdA03
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)