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- PDB-5dzd: Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide -

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Basic information

Entry
Database: PDB / ID: 5dzd
TitleCrystal Structure of WW4 domain of ITCH in complex with TXNIP peptide
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Thioredoxin-interacting protein
KeywordsLIGASE/PROTEIN BINDING / structural genomics / Structural Genomics Consortium / SGC / LIGASE-PROTEIN BINDING complex
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 / regulation of necroptotic process ...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 / regulation of necroptotic process / negative regulation of cell division / CXCR chemokine receptor binding / 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 / protein K63-linked ubiquitination / response to mechanical stimulus / response to glucose / Purinergic signaling in leishmaniasis infection / protein autoubiquitination / keratinocyte differentiation / response to progesterone / protein K48-linked ubiquitination / Downregulation of ERBB4 signaling / enzyme inhibitor activity / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of canonical NF-kappaB signal transduction / response to hydrogen peroxide / Negative regulators of DDX58/IFIH1 signaling / 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 / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / ubiquitin protein ligase activity / response to estradiol / regulation of cell population proliferation / Antigen processing: Ubiquitination & Proteasome degradation / 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 / symbiont entry into host cell / ubiquitin protein ligase binding / 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: 1.57 Å
AuthorsLiu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide
Authors: Liu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionOct 14, 2015ID: 4ROI
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Sep 27, 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 / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)13,72521
Polymers13,7254
Non-polymers017
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area6370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.668, 52.668, 82.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-705-

HOH

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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: 5503.151 Da / Num. of mol.: 2 / Fragment: UNP residues 324-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: custom / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / txnip / Thioredoxin-binding protein 2 / Vitamin D3 up-regulated protein 1


Mass: 1359.589 Da / Num. of mol.: 2 / Fragment: UNP residues 327-338 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 17 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2 M sodium formate, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→37.24 Å / Num. obs: 16849 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.043 / Net I/σ(I): 42.7 / Num. measured all: 223544 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.57-1.612.60.4975.8102858180.9580.1440.51899.7
8.61-37.249.10.018103.8126914010.0060.01999.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata scaling
Aimless0.5.15data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YSF

2ysf


Resolution: 1.57→37.24 Å / SU B: 1.155 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.078
Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. REFINEMENT RESTRAINTS FOR THE ACETYL AND AMIDE PROTECTED PEPTIDE TERMINI WERE PREPARED WITH JLIGAND. COOT WAS USED FOR INTERACTIVE MODEL ...Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. REFINEMENT RESTRAINTS FOR THE ACETYL AND AMIDE PROTECTED PEPTIDE TERMINI WERE PREPARED WITH JLIGAND. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 800 4.8 %THIN SHELLS (SFTOOLS)
Rwork0.175 ---
obs0.176 15998 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.57→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 19 60 866

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