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- PDB-4rof: Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide -

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Basic information

Entry
Database: PDB / ID: 4rof
TitleCrystal Structure of WW3 domain of ITCH in complex with TXNIP peptide
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Thioredoxin-interacting protein
KeywordsLIGASE / Structural Genomics / Structural GenomicsConsortium / SGC / Structural Genomics Consortium
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / cellular response to tumor cell / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of defense response to virus / protein K29-linked ubiquitination / T cell anergy / cellular response to oxidised low-density lipoprotein particle stimulus / CXCR chemokine receptor binding ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / cellular response to tumor cell / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of defense response to virus / protein K29-linked ubiquitination / T cell anergy / cellular response to oxidised low-density lipoprotein particle stimulus / CXCR chemokine receptor binding / regulation of necroptotic process / negative regulation of cell division / protein branched polyubiquitination / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / HECT-type E3 ubiquitin transferase / arrestin family protein binding / Regulation of FOXO transcriptional activity by acetylation / regulation of hematopoietic stem cell differentiation / negative regulation of JNK cascade / positive regulation of receptor catabolic process / ubiquitin-ubiquitin ligase activity / negative regulation of type I interferon production / ligase activity / platelet-derived growth factor receptor signaling pathway / ubiquitin-like protein ligase binding / The NLRP3 inflammasome / protein monoubiquitination / ribonucleoprotein complex binding / response to mechanical stimulus / protein K63-linked ubiquitination / response to glucose / Purinergic signaling in leishmaniasis infection / protein autoubiquitination / keratinocyte differentiation / protein K48-linked ubiquitination / response to progesterone / enzyme inhibitor activity / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of canonical NF-kappaB signal transduction / Negative regulators of DDX58/IFIH1 signaling / response to hydrogen peroxide / regulation of cell growth / Cytoprotection by HMOX1 / Degradation of GLI1 by the proteasome / NOD1/2 Signaling Pathway / Hedgehog 'on' state / receptor internalization / response to calcium ion / Regulation of necroptotic cell death / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / response to estradiol / Antigen processing: Ubiquitination & Proteasome degradation / regulation of cell population proliferation / protein transport / RUNX1 regulates transcription of genes involved in differentiation of HSCs / response to oxidative stress / cytoplasmic vesicle / early endosome membrane / cell cortex / defense response to virus / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of apoptotic process / response to xenobiotic stimulus / inflammatory response / innate immune response / apoptotic process / ubiquitin protein ligase binding / symbiont entry into host cell / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / E3 ubiquitin-protein ligase, SMURF1 type / : / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / HECT domain ...: / E3 ubiquitin-protein ligase, SMURF1 type / : / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / WW domain / C2 domain profile. / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin E-set
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy homolog / Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of WW3 domain of ITCH in complex with TXNIP peptide
Authors: Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 homolog
B: E3 ubiquitin-protein ligase Itchy homolog
C: Thioredoxin-interacting protein
D: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)13,5434
Polymers13,5434
Non-polymers00
Water18010
1
A: E3 ubiquitin-protein ligase Itchy homolog
C: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)6,7722
Polymers6,7722
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area3290 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase Itchy homolog
D: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)6,7722
Polymers6,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4 kcal/mol
Surface area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.171, 55.312, 59.796
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 5411.962 Da / Num. of mol.: 2 / Fragment: UNP residues 436-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: custom / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2
References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Thioredoxin-interacting protein / Thioredoxin-binding protein 2 / Vitamin D3 up-regulated protein 1 / TXNIP peptide


Mass: 1359.589 Da / Num. of mol.: 2 / Fragment: UNP residues 327-338 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.84 Å3/Da / Density % sol: 33.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate pH 5.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→40 Å / Num. obs: 6898 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.103 / Χ2: 1.728 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.03-2.075.70.9973161.009199.7
2.07-2.16.20.8823371.1041100
2.1-2.146.40.7613381.1251100
2.14-2.196.60.7433321.2311100
2.19-2.236.50.8773391.2531100
2.23-2.296.40.4623331.9161100
2.29-2.346.70.4913501.2751100
2.34-2.416.70.3663291.2331100
2.41-2.486.80.3583421.3191100
2.48-2.566.70.3043411.4091100
2.56-2.656.70.2653391.4831100
2.65-2.756.70.2113521.6241100
2.75-2.886.80.183301.641100
2.88-3.036.70.1493561.7661100
3.03-3.226.80.1093381.8521100
3.22-3.476.60.0843512.261100
3.47-3.826.30.0623532.5381100
3.82-4.376.40.0623572.7311100
4.37-5.516.40.0523612.51199.4
5.51-405.70.0564043.062199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F21

2f21


Resolution: 2.03→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2734 / WRfactor Rwork: 0.2257 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7465 / SU B: 14.984 / SU ML: 0.188 / SU R Cruickshank DPI: 0.2659 / SU Rfree: 0.2292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DIFFRACTION IMAGES SHOWED MUTLIPLE PATTERNS AND ICE RINGS. FOR INTEGRATION, DIFFRACTION IMAGES WERE SEPARATED INTO RANGES (PHI 0 THROUGH 63 DEGREES, 63 THROUGH 180 DEGREES, RESPECTIVELY). ...Details: DIFFRACTION IMAGES SHOWED MUTLIPLE PATTERNS AND ICE RINGS. FOR INTEGRATION, DIFFRACTION IMAGES WERE SEPARATED INTO RANGES (PHI 0 THROUGH 63 DEGREES, 63 THROUGH 180 DEGREES, RESPECTIVELY). MOSAICITY AND CRYSTAL-TO-DETECTOR DISTANCE WERE CONSTRAINED DURING INTEGRATION. NO-MERGE-ORIGINAL-INDEX REFLECTIONS FROM SCALEPACK WERE MERGED WITH AIMLESS (ONLYMERGE). ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING AND MAP IMPROVEMENT. PARROT WAS USED FOR PHASE IMPROVEMENT. RESTRAINTS FOR THE C-TERMINAL AMIDE PROTECTION OF THE PEPTIDE LIGAND WERE PREPARED WITH JLIGAND. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2975 943 13.8 %THIN SHELLS (SFTOOLS)
Rwork0.2389 ---
obs0.2463 6841 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.68 Å2 / Biso mean: 38.9429 Å2 / Biso min: 23.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0 Å2
2--2.32 Å2-0 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms744 0 0 10 754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02783
X-RAY DIFFRACTIONr_bond_other_d0.0010.02710
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9391074
X-RAY DIFFRACTIONr_angle_other_deg0.81931625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.004592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.1152340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95915108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.673158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2108
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02187
X-RAY DIFFRACTIONr_mcbond_it2.1082.705376
X-RAY DIFFRACTIONr_mcbond_other2.1122.708374
X-RAY DIFFRACTIONr_mcangle_it2.8514.035466
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 120 -
Rwork0.286 350 -
all-470 -
obs--98.53 %
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)
14.51631.17962.04048.23122.52256.4829-0.10480.34670.0291-0.0102-0.17020.0044-0.3361-0.17740.27490.02840.0122-0.00920.0526-0.00760.01882.775.58912.011
24.435-0.52010.99563.0992-0.67877.478-0.2195-0.0242-0.0060.0431-0.10430.1687-0.24390.20050.32380.0415-0.0138-0.01180.01230.00470.0275-18.9945.92828.644
38.6882.89365.35143.57861.04478.52390.0424-0.1404-0.24490.0940.0513-0.11570.21970.1297-0.09370.07240.0180.00850.0984-0.00430.123-3.0170.80819.116
48.4101-4.9864.0578.75935.063211.77070.37180.4476-0.6629-0.3069-0.10010.44630.26470.5726-0.27170.20260.0914-0.03280.1968-0.01070.1157-12.272.20521.408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A437 - 472
2X-RAY DIFFRACTION2B437 - 472
3X-RAY DIFFRACTION3C329 - 338
4X-RAY DIFFRACTION3C339
5X-RAY DIFFRACTION4D329 - 338
6X-RAY DIFFRACTION4D339

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