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- PDB-2nq3: Crystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiq... -

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Basic information

Entry
Database: PDB / ID: 2nq3
TitleCrystal structure of the C2 Domain of Human Itchy Homolog E3 Ubiquitin Protein Ligase
ComponentsItchy homolog E3 ubiquitin protein ligase
KeywordsLIGASE / C2 DOMAIN / UBL CONJUGATION PATHWAY / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein K29-linked ubiquitination / T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process / positive regulation of T cell anergy ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein K29-linked ubiquitination / T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process / positive regulation of T cell anergy / protein branched polyubiquitination / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / HECT-type E3 ubiquitin transferase / negative regulation of JNK cascade / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / positive regulation of receptor catabolic process / ligase activity / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / protein monoubiquitination / ribonucleoprotein complex binding / protein K48-linked ubiquitination / protein autoubiquitination / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / receptor internalization / Regulation of necroptotic cell death / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / ubiquitin-dependent protein catabolic process / early endosome membrane / cytoplasmic vesicle / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / inflammatory response / symbiont entry into host cell / innate immune response / intracellular membrane-bounded organelle / apoptotic process / negative regulation of apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain ...E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Butler-Cole, C. / Finerty Jr., P.J. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Citation
#1: Journal: Genomics / Year: 2001
Title: Human ITCH is a coregulator of the hematopoietic transcription factor NF-E2
Authors: Chen, X. / Wen, S. / Fukuda, M.N. / Gavva, N.R. / Hsu, D. / Akama, T.O. / Yang-Feng, T. / Shen, C.K.
#2: Journal: Mol.Cell.Neurosci. / Year: 1998
Title: Atrophin-1, the DRPLA gene product, interacts with two families of WW domain-containing proteins
Authors: Wood, J.D. / Yuan, J. / Margolis, R.L. / Colomer, V. / Duan, K. / Kushi, J. / Kaminsky, Z. / Kleiderlein, J.J. / Sharp, A.H. / Ross, C.A.
#3: Journal: Mol.Cell.Biol. / Year: 2000
Title: Latent membrane protein 2A of Epstein-Barr virus binds WW domain E3 protein-ubiquitin ligases that ubiquitinate B-cell tyrosine kinases
Authors: Winberg, G. / Matskova, L. / Chen, F. / Plant, P. / Rotin, D. / Gish, G. / Ingham, R. / Ernberg, I. / Pawson, T.
#4: Journal: J.Biol.Chem. / Year: 2002
Title: Interaction between two ubiquitin-protein isopeptide ligases of different classes, CBLC and AIP4/ITCH
Authors: Courbard, J.R. / Fiore, F. / Adelaide, J. / Borg, J.P. / Birnbaum, D. / Ollendorff, V.
History
DepositionOct 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Itchy homolog E3 ubiquitin protein ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2372
Polymers19,2021
Non-polymers351
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.499, 82.499, 65.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-180-

HOH

21A-197-

HOH

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Components

#1: Protein Itchy homolog E3 ubiquitin protein ligase / Itch / Atrophin-1-interacting protein 4 / AIP4 / NFE2-associated polypeptide 1 / NAPP1


Mass: 19201.719 Da / Num. of mol.: 1 / Fragment: C2 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: p28a-LIC-TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 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 ...Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 24173 / Num. obs: 24173 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rsym value: 0.09 / Net I/σ(I): 29.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1192 / Rsym value: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FK9

2fk9


Resolution: 1.8→24.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.103 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.082
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19544 1233 5.1 %RANDOM
Rwork0.16194 ---
obs0.16352 22908 99.98 %-
all-24145 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 1 128 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221086
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9681484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.75827.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90415202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.428151
X-RAY DIFFRACTIONr_chiral_restr0.1380.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02795
X-RAY DIFFRACTIONr_nbd_refined0.2010.2424
X-RAY DIFFRACTIONr_nbtor_refined0.310.2756
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2107
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.214
X-RAY DIFFRACTIONr_mcbond_it2.0443704
X-RAY DIFFRACTIONr_mcangle_it2.91841130
X-RAY DIFFRACTIONr_scbond_it3.755433
X-RAY DIFFRACTIONr_scangle_it5.917354
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 93 -
Rwork0.229 1662 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.03020.8144-1.39932.1813-0.84234.0457-0.030.12130.37910.07350.09950.3265-0.1086-0.3623-0.0695-0.00430.01280.0061-0.0005-0.00190.0479-4.747651.2025-1.7644
22.8757-2.16842.71253.1376-3.19074.9909-0.06070.02280.0621-0.02190.0581-0.0257-0.02380.04170.0025-0.00960.0027-0.00340.0174-0.00210.030210.701345.90646.5102
328.4733-11.1477-8.1625.097612.264319.5583-1.1022-1.4005-1.94341.96830.5934-0.13591.95140.81480.50880.22140.1254-0.00860.20780.0820.156415.092530.406319.8682
415.2756-4.04434.98261.0712-1.26019.05680.0835-1.454-0.97940.3230.34810.06161.20531.1572-0.43150.11840.1863-0.04140.26510.08870.111622.221125.426114.4267
51.47-0.520.47420.7083-0.31571.2456-0.0288-0.0566-0.0980.03690.0256-0.0310.08690.14330.00320.0010.02560.00280.00840.0010.03511.859335.47084.8396
610.0504-0.33682.505712.6818-7.249216.15910.0244-0.30270.18520.5276-0.2612-0.4397-0.38660.88290.2368-0.0384-0.0011-0.00320.0433-0.01130.008817.094342.09497.6606
70.04020.1253-0.24060.96710.28093.2894-0.08150.21370.030.04750.01970.00470.0055-0.14670.06190.00070.00340.0042-0.0040.01120.0276-0.085246.62250.2019
815.0064-10.13385.261113.6221-4.70626.78140.06570.133-0.8597-0.09110.05950.63530.1851-0.0608-0.1252-0.0158-0.00820.0072-0.0244-0.0040.02450.44337.70416.8784
99.6615-2.7325-3.989513.53315.21416.5018-0.18750.1418-0.2266-0.24480.2037-0.63790.48860.4019-0.01620.04040.0350.0149-0.00350.01660.019912.766627.89045.7548
1015.33360.3113-7.26047.42461.6727.8648-0.32-0.1844-0.97580.52580.15920.13940.59270.26790.16070.03650.0243-0.0016-0.0352-0.00920.070913.913321.14892.2774
111.3436-1.2663-0.31572.37870.41931.1457-0.0142-0.0033-0.0692-0.0020.02030.1005-0.0249-0.0209-0.00610.00530.00250.01080.0170.01250.0299-0.74343.382511.1462
1215.0418-5.4292-2.03317.13041.08125.06030.18840.27190.7645-0.0505-0.078-0.3518-0.46510.066-0.11030.0851-0.0058-0.0025-0.00640.01410.08510.937457.83599.3459
131.6590.7423-0.33857.2097-1.74912.66950.0014-0.0201-0.04040.2092-0.0178-0.01020.05790.00610.01640.00880.00910.00060.0140.00520.03045.564141.840615.5027
140.90722.90667.181211.217331.996299.2569-0.71470.1714-0.63441.9614-2.0153-0.18195.6207-3.77422.730.533-0.23040.24320.1667-0.0930.04841.384226.39418.3879
151.73940.7336-0.5787.9942-3.60263.825-0.0352-0.1054-0.05420.25810.03870.0846-0.05440.0177-0.00350.01870.02350.00630.0351-0.00590.04098.106440.712314.3248
1634.3151-5.4519-3.30096.1783-0.026911.06310.18190.53941.3363-0.0776-0.11770.3188-0.6355-0.9424-0.06410.04450.0269-0.0099-0.03880.01520.0413-2.126856.60293.7621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 2031 - 38
2X-RAY DIFFRACTION2AA21 - 2739 - 45
3X-RAY DIFFRACTION3AA28 - 3346 - 51
4X-RAY DIFFRACTION4AA36 - 4054 - 58
5X-RAY DIFFRACTION5AA41 - 6359 - 81
6X-RAY DIFFRACTION6AA64 - 6782 - 85
7X-RAY DIFFRACTION7AA68 - 7786 - 95
8X-RAY DIFFRACTION8AA78 - 8296 - 100
9X-RAY DIFFRACTION9AA83 - 87101 - 105
10X-RAY DIFFRACTION10AA88 - 92106 - 110
11X-RAY DIFFRACTION11AA93 - 109111 - 127
12X-RAY DIFFRACTION12AA110 - 115128 - 133
13X-RAY DIFFRACTION13AA116 - 124134 - 142
14X-RAY DIFFRACTION14AA125 - 130143 - 148
15X-RAY DIFFRACTION15AA131 - 139149 - 157
16X-RAY DIFFRACTION16AA140 - 145158 - 163

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