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- PDB-5dws: Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide -

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Basic information

Entry
Database: PDB / ID: 5dws
TitleCrystal Structure of ITCH WW3 domain in complex with TXNIP peptide
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • txnip
KeywordsLIGASE / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / cellular response to tumor cell / protein K29-linked ubiquitination / T cell anergy / positive regulation of T cell anergy / cellular response to oxidised low-density lipoprotein particle stimulus ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / cellular response to tumor cell / protein K29-linked ubiquitination / T cell anergy / positive regulation of 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 / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / enzyme inhibitor activity / Regulation of FOXO transcriptional activity by acetylation / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon production / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein monoubiquitination / protein K63-linked ubiquitination / ligase activity / platelet-derived growth factor receptor signaling pathway / The NLRP3 inflammasome / protein autoubiquitination / protein K48-linked ubiquitination / response to glucose / Purinergic signaling in leishmaniasis infection / ribonucleoprotein complex binding / response to mechanical stimulus / keratinocyte differentiation / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / response to progesterone / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / response to hydrogen peroxide / receptor internalization / Regulation of necroptotic cell death / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / 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 / protein transport / response to estradiol / RUNX1 regulates transcription of genes involved in differentiation of HSCs / regulation of cell population proliferation / cell cortex / early endosome membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / inflammatory response / symbiont entry into host cell / positive regulation of apoptotic process / cell cycle / intracellular membrane-bounded organelle / innate immune response / apoptotic process / 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 / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / 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 ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / 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 / 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 / Single Sheet / C2 domain superfamily / Immunoglobulin E-set / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy homolog / Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 ITCH WW3 domain in complex with TXNIP peptide
Authors: Liu, Y. / Tempel, W. / Dong, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionOct 14, 2015ID: 4RRE
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 / 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 homolog
B: txnip
C: E3 ubiquitin-protein ligase Itchy homolog
D: txnip
E: E3 ubiquitin-protein ligase Itchy homolog
F: txnip
G: E3 ubiquitin-protein ligase Itchy homolog
H: txnip


Theoretical massNumber of molelcules
Total (without water)27,08634
Polymers27,0868
Non-polymers026
Water1,31573
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-31 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.733, 30.142, 60.755
Angle α, β, γ (deg.)90.00, 109.20, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4 / Fragment: UNP residues 285-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / 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
txnip


Mass: 1359.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7*PLUS
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 26 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.65→30.14 Å / Num. obs: 24552 / % possible obs: 98.1 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 14.3 / Num. measured all: 91039 / Scaling rejects: 23
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.683.70.5162.3435311690.7930.3080.60294.6
9.03-30.1430.0332.15111680.9970.020.03693

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
Aimless0.5.12data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ROF

4rof


Resolution: 1.65→30 Å / Cross valid method: THROUGHOUT
Details: COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1252 5.1 %THIN SHELLS (SFTOOLS)
Rwork0.222 ---
obs0.224 23283 97.8 %-
Displacement parametersBiso mean: 26.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20.44 Å2
2---1.33 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1505 0 30 73 1608
LS refinement shellResolution: 1.65→1.69 Å
RfactorNum. reflection% reflection
Rwork0.248 1778 -
obs--96.84 %

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