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- PDB-5xmc: Crystal structure of the auto-inhibited Nedd4 family E3 ligase Itch -

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Basic information

Entry
Database: PDB / ID: 5xmc
TitleCrystal structure of the auto-inhibited Nedd4 family E3 ligase Itch
ComponentsE3 ubiquitin-protein ligase Itchy
KeywordsLIGASE / Auto-inhibited Itch
Function / homology
Function and homology information


regulation of protein deubiquitination / Downregulation of ERBB4 signaling / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of necroptotic cell death / negative regulation of defense response to virus / Degradation of GLI1 by the proteasome / protein K29-linked ubiquitination / Hedgehog 'on' state / T cell anergy ...regulation of protein deubiquitination / Downregulation of ERBB4 signaling / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of necroptotic cell death / negative regulation of defense response to virus / Degradation of GLI1 by the proteasome / protein K29-linked ubiquitination / Hedgehog 'on' state / T cell anergy / positive regulation of T cell anergy / RUNX1 regulates transcription of genes involved in differentiation of HSCs / CXCR chemokine receptor binding / CD4-positive, alpha-beta T cell proliferation / NOD1/2 Signaling Pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of CD4-positive, alpha-beta T cell proliferation / HECT-type E3 ubiquitin transferase / negative regulation of JNK cascade / arrestin family protein binding / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / protein monoubiquitination / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / ligase activity / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / ribonucleoprotein complex binding / protein catabolic process / receptor internalization / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / cell cortex / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / early endosome membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / intracellular membrane-bounded organelle / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / membrane / nucleus / 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) / WW domain / WW/rsp5/WWP domain signature. ...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) / 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
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
Model detailsAllosteric auto-inhibition and activation of Nedd4 family E3 ligase Itch
AuthorsShan, Z. / Wen, W.
CitationJournal: EMBO Rep. / Year: 2017
Title: Allosteric auto-inhibition and activation of the Nedd4 family E3 ligase Itch
Authors: Zhu, K. / Shan, Z. / Chen, X. / Cai, Y. / Cui, L. / Yao, W. / Wang, Z. / Shi, P. / Tian, C. / Lou, J. / Xie, Y. / Wen, W.
History
DepositionMay 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Itchy


Theoretical massNumber of molelcules
Total (without water)83,4121
Polymers83,4121
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.586, 77.084, 130.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase Itchy / HECT-type E3 ubiquitin transferase Itchy homolog


Mass: 83412.203 Da / Num. of mol.: 1 / Fragment: Nedd4 family E3 ligase Itch, UNP residues 143-864
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itch / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q8C863, HECT-type E3 ubiquitin transferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5
Details: 50mM citric acid, 50mM Bis-Tris propone, pH 5.5, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22580 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Rrim(I) all: 0.08 / Χ2: 0.895 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.644.80.4980.8220.250.5590.925100
2.64-2.694.70.4920.8490.250.5540.867100
2.69-2.744.50.3730.860.1950.4220.92100
2.74-2.84.40.3320.9230.1770.3780.893100
2.8-2.864.60.2790.9430.1440.3150.92999.9
2.86-2.934.70.2540.9490.130.2860.869100
2.93-35.10.1910.9720.0930.2130.909100
3-3.085.10.1760.9730.0850.1960.887100
3.08-3.1750.1510.9820.0740.1690.913100
3.17-3.2850.1230.9840.060.1370.92199.8
3.28-3.3950.1070.9880.0530.1190.94799.8
3.39-3.534.90.0920.990.0450.1030.98499.8
3.53-3.694.80.0830.9920.0410.0930.976100
3.69-3.884.60.0710.9920.0360.080.90899.9
3.88-4.134.30.0580.9940.0310.0660.82599.9
4.13-4.454.60.0570.9950.0290.0640.9399.7
4.45-4.8950.0520.9950.0250.0580.90299
4.89-5.64.90.050.9960.0240.0550.84899.2
5.6-7.054.60.0470.9940.0240.0530.72999.3
7.05-504.30.0420.9970.0210.0470.80398.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TUG

3tug


Resolution: 2.6→47.593 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.95
RfactorNum. reflection% reflection
Rfree0.2621 1098 5.09 %
Rwork0.2135 --
obs0.2159 21563 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.9 Å2 / Biso mean: 46.12 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 2.6→47.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 46 3322
Biso mean---27.45 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083401
X-RAY DIFFRACTIONf_angle_d1.0594622
X-RAY DIFFRACTIONf_chiral_restr0.077476
X-RAY DIFFRACTIONf_plane_restr0.005602
X-RAY DIFFRACTIONf_dihedral_angle_d16.2851200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.71840.33961050.26292090219581
2.7184-2.86170.31751450.24752511265697
2.8617-3.04090.26131360.234225882724100
3.0409-3.27570.29541320.233626112743100
3.2757-3.60520.25191360.205926362772100
3.6052-4.12660.22991580.192126122770100
4.1266-5.19810.23911380.17752657279599
5.1981-47.60090.26881480.22922760290899
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)
10.8671-0.9241-0.65621.16381.23382.2490.04330.12610.082-0.0421-0.1072-0.08860.083-0.01520.07140.2827-0.03980.07120.25280.06250.24448.2714-10.0217-44.2425
22.5239-0.391-0.66784.40630.90564.211-0.02250.2018-0.072-0.3412-0.05930.0110.169-0.32290.04080.2324-0.0190.01370.2282-0.02980.1462-1.2292-1.5285-35.5687
32.3388-0.81841.02571.16480.46162.3195-0.05440.0297-0.0343-0.3124-0.0045-0.7895-0.10830.812-0.39510.2894-0.00850.16980.47350.05630.575815.5133.631-31.3617
41.7178-0.51920.46531.11610.33931.8024-0.0517-0.5232-0.16250.63950.3549-0.43550.93010.6142-0.09510.75640.2918-0.17670.6114-0.06720.331611.3573-6.2988-10.9644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 287 through 503 )A287 - 503
2X-RAY DIFFRACTION2chain 'A' and (resid 504 through 635 )A504 - 635
3X-RAY DIFFRACTION3chain 'A' and (resid 636 through 725 )A636 - 725
4X-RAY DIFFRACTION4chain 'A' and (resid 726 through 859 )A726 - 859

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