SAXSdb — 2nq3

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

Itchy homolog E3 ubiquitin protein ligase

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–155	Fragment：C2 Domain	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

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 2NQ3	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 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 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
2P4R Structural basis for a novel interaction between AIP4 and beta-PIX Deposited 2007-03-13	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 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 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 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 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 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 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 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 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
5DWS Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide Deposited 2015-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 285–323（39 aa） Fragment：UNP residues 285-323 Chain C 285–323（39 aa） Fragment：UNP residues 285-323 Chain E 285–323（39 aa） Fragment：UNP residues 285-323 Chain G 285–323（39 aa） Fragment：UNP residues 285-323	Not recorded	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
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 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 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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 19–173； UniProt 1–155

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nq3
Deposition date deposition_date	2006-10-30
Structure title title	Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase
Keywords keywords	C2 DOMAIN, LIGASE, UBL CONJUGATION PATHWAY, STRUCTURAL GENOMICS CONSORTIUM, SGC; 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	16.55 Å
Radius of gyration Rg (electron density) rg_electron	15.53 Å
Forward intensity I(0) i0	3936570.00
Molecular weight molecular_weight	14471.0 kDa
Excluded volume excluded_volume	18292 Å³
Envelope volume envelope_volume	21378 Å³
Hydration-shell volume shell_volume	12167 Å³
Envelope diameter envelope_diameter	57.7 Å
Shell Rg shell_rg	20.83 Å
Envelope Rg envelope_rg	16.14 Å
Shape Rg shape_rg	15.52 Å
Total Rg total_rg	16.62 Å
Total atoms total_atoms	1015
Residues n_residues	131
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	60.6 Å
Rg (real space) rg_real	16.57 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	3.9370e+06
I(0) uncertainty (real space) i0_real_error	5.0400e+04
Rg (reciprocal space) rg_reciprocal	16.56 Å
I(0) (reciprocal space) i0_reciprocal	3937000.0000
Solution quality estimate total_estimate	0.8247
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	59.0 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.147
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	830100.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.598; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Itchy homolog E3 ubiquitin protein ligase
Molecular weight formula_weight	19201.7 kDa
EC 编号 ec_number	6.3.2.-
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	1192

MHHHHHHSSGRENLYFQGMSDSGSQLGSMGSLTMKSQLQITVISAKLKENKKNWFGPSPYVEVTVDGQSKKTEKCNNTNSPKWKQPLTVIVTPVSKLHFRVWSHQTLKSDVLLGTAALDIYETLKSNNMKLEEVVVTLQLGGDKEPTETIGDLSICLDGLQLESEVVTNGETT

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)

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2nq3a1
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.1 — PLC-like (P variant)

CATH v4.4 (1 domains)

Domain ID domain_id	2nq3A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (5)

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Unit-cell length a length_a	82.499 Å
Unit-cell length b length_b	82.499 Å
Unit-cell length c length_c	65.273 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	24.100 Å
R factor r_factor	0.1635
R_work r_work	0.1619
R_free r_free	0.1954

fit	/app/data/saxs_computation/nq/2nq3/2nq3.fit
pddf	/app/data/pr_computation/nq/2nq3/2nq3.pr.out
profile	/app/data/saxs_computation/nq/2nq3/2nq3.dat

Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase

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

Itchy homolog E3 ubiquitin protein ligase

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