E3 ubiquitin-protein ligase Itchy homolog
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 × 8 PDB declaration: octameric（8） Consistent with protein copy count | Chain A； UniProt 285–323 Chain C； UniProt 285–323 Chain E； UniProt 285–323 Chain G； UniProt 285–323 | Fragment：UNP residues 285-323 | txnip × 4 UNX UNKNOWN LIGAND × 26 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293 K；20% PEG-3350, 0.2 M sodium acetate | Resolution 1.65 Å R-free 0.257 |
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 5DWS | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2DMV Solution structure of the second ww domain of Itchy homolog E3 ubiquitin protein ligase (Itch) Deposited 2006-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
328–357（30 aa）
Fragment：WW domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition
1.4mM protein U-15N, 13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT;
0.02% NaN3; 10% D2O, 90% H2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2KYK The sandwich region between two LMP2A PY motif regulates the interaction between AIP4WW2domain and PY motif Deposited 2010-05-28 | 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
359–392（34 aa）
Fragment：WW 2 domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；303 K；Pressure ambient
NMR sample composition
0.01% [U-95% 13C; U-95% 15N] sodium phosphate-1, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2NQ3 Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase Deposited 2006-10-30 | 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
1–155（155 aa）
Fragment：C2 Domain
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein at 20 mg/ml was dissolved in 20 mM Tris-HCl, pH 8.0, 0.15 M NaCl, 5%
glycerol, 2 mM DTT, and mixed 1:1 with well solution that was 20% PEG3350,
0.1 M bis-Tris, pH 6.0, 0.2 M NH4OAc, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
|
Resolution 1.80 Å R-free 0.195 |
| 2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13 | 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 T
246–270（25 aa）
Fragment：AIP4 (209-224)
|
Not recorded | SO4 SULFATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.246 |
| 2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13 | 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 T
246–270（25 aa）
Fragment：AIP4 (209-224)
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M TrisHCl, 0.2 M ammonium sulfate, 32-38% (w/v) PEG-MME 5000, pH 7.1-7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.246 |
| 2YSF Solution structure of the fourth WW domain from the human E3 ubiquitin-protein ligase Itchy homolog, ITCH Deposited 2007-04-03 | 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
480–512（33 aa）
Fragment：WW domain, UNP residues 480-512
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition
0.9mM sample U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 3TUG Crystal structure of the HECT domain of ITCH E3 ubiquitin ligase Deposited 2011-09-16 | 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
524–903（380 aa）
|
Not recorded | CL CHLORIDE ION × 1 UNX UNKNOWN LIGAND × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；30% PEG1500, 0.2M NaCl 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
|
Resolution 2.27 Å R-free 0.256 |
| 4ROF Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide Deposited 2014-10-28 | 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
436–474（39 aa）
Fragment：UNP residues 436-474
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.03 Å R-free 0.297 |
| 4ROF Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide Deposited 2014-10-28 | 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 B
436–474（39 aa）
Fragment：UNP residues 436-474
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, vapor diffusion, sitting drop, temperature 293K
|
Resolution 2.03 Å R-free 0.297 |
| 5C7M CRYSTAL STRUCTURE OF E3 LIGASE ITCH WITH A UB VARIANT Deposited 2015-06-24 | 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
524–899（376 aa）
Fragment：HECT DOMAIN (UNP RESIDUES 524-899)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；The ITCH and ubiquitin variant ubv.it.02 were mixed at molarity ratio 1:2, and then concentrated to 17mg/ml.
The protein sample was mixed with 1mg/mL chymotrypsin at a 1:1000 (W/W) chymotrypsin:protein ratio right before set up crystallization. Crystal was initially obtained from SGC-I screen condition A05. Crystal used for structure refinement was grown in 1.6M NH4SO4, 0.2M NaAc, 0.1M HEPES pH 7.5, 5% Ethylene Glycol in hanging drop setup, using 1.2uL protein, 1.2uL well solution over 0.5 mL reservoir buffer at 20 C. Crystals grow to mountable size for ~1 weeks. Harvested crystal was flash-frozen in liquid nitrogen. A well solution containing 20% glycerol was used as the cryo-protectant
|
Resolution 3.03 Å R-free 0.297 |
| 5CQ2 Crystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide Deposited 2015-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
282–370（89 aa）
Fragment：UNP residues 282-370
|
Not recorded | UNX UNKNOWN LIGAND × 72 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；30% PEG4000, 0.2 M magnesium chloride, 0.1 M TRIS
|
Resolution 1.40 Å R-free 0.184 |
| 5DZD Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide Deposited 2015-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
324–363（40 aa）
Fragment：UNP residues 324-363
Chain B
324–363（40 aa）
Fragment：UNP residues 324-363
|
Not recorded | UNX UNKNOWN LIGAND × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；2 M sodium formate, 0.1 M Tris, pH 8.5
|
Resolution 1.57 Å R-free 0.206 |
| 5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
249–269（21 aa）
Fragment：UNP residues 249-269
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500
|
Resolution 1.65 Å R-free 0.161 |
| 5SXP STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX Deposited 2016-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
249–269（21 aa）
Fragment：UNP residues 249-269
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MIB buffer pH 5.0 and 25% PEG1500
|
Resolution 1.65 Å R-free 0.161 |
11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | ITCH_HUMAN |
| Isoform | Q96J02-3 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 9–47； UniProt 285–323 Author chain C； PDBConstruct 9–47； UniProt 285–323 Author chain E； PDBConstruct 9–47； UniProt 285–323 Author chain G； PDBConstruct 9–47； UniProt 285–323 |