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- PDB-5cq2: Crystal Structure of tandem WW domains of ITCH in complex with TX... -

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Basic information

Entry
Database: PDB / ID: 5cq2
TitleCrystal Structure of tandem WW domains of ITCH in complex with TXNIP peptide
Components
  • E3 ubiquitin-protein ligase Itchy homolog
  • Thioredoxin-interacting protein
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 / 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 / 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 / negative regulation of cell division / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / CXCR chemokine receptor binding / HECT-type E3 ubiquitin transferase / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / 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 / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ribonucleoprotein complex binding / response to glucose / Purinergic signaling in leishmaniasis infection / 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 / Regulation of necroptotic cell death / receptor internalization / Cytoprotection by HMOX1 / response to calcium ion / protein import into nucleus / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / 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 / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / early endosome membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / cell cycle / inflammatory response / symbiont entry into host cell / positive regulation of apoptotic process / innate immune response / intracellular membrane-bounded organelle / 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
E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; - #10 / 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 ...E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; - #10 / 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. / WW domain superfamily / C2 domain / C2 domain profile. / 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 / Resolution: 1.4 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2016
Title: Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP.
Authors: Liu, Y. / Lau, J. / Li, W. / Tempel, W. / Li, L. / Dong, A. / Narula, A. / Qin, S. / Min, J.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
SupersessionOct 14, 2015ID: 4ROH
Revision 1.1Oct 14, 2015Group: Other
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Sep 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Thioredoxin-interacting protein
C: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)13,13221
Polymers13,1323
Non-polymers018
Water99155
1
A: E3 ubiquitin-protein ligase Itchy homolog
B: Thioredoxin-interacting protein
C: Thioredoxin-interacting protein

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

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

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


Theoretical massNumber of molelcules
Total (without water)52,52684
Polymers52,52612
Non-polymers072
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area17330 Å2
ΔGint-99 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.277, 62.260, 67.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

DetailsAs per the authors the biologically relevant macromolecular assembly is not applicable to this protein fragment

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Components

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


Mass: 10412.411 Da / Num. of mol.: 1 / Fragment: UNP residues 282-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITCH / Plasmid: pET28-MHL / 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


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.: 18 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 30% PEG4000, 0.2 M magnesium chloride, 0.1 M TRIS

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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 315r / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.4→45.86 Å / Num. obs: 24240 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 25.1 / Num. measured all: 172053
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
1.4-1.426.50.9272771911910.8070.3951.008100
7.67-45.865.10.01967.381815910.0090.02190.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
Aimless0.5.12data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RRE

4rre
PDB Unreleased entry


Resolution: 1.4→45.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.233 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18374 1144 4.7 %RANDOM
Rwork0.15336 ---
obs0.15479 23096 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0 Å2-0 Å2
2--1.59 Å2-0 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms785 0 18 55 858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02842
X-RAY DIFFRACTIONr_bond_other_d0.0030.02744
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.971155
X-RAY DIFFRACTIONr_angle_other_deg1.07931735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.8122.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.96215125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.017158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022944
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02188
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5322.383406
X-RAY DIFFRACTIONr_mcbond_other3.5222.374404
X-RAY DIFFRACTIONr_mcangle_it4.7563.557505
X-RAY DIFFRACTIONr_mcangle_other4.753.553505
X-RAY DIFFRACTIONr_scbond_it3.0952.406434
X-RAY DIFFRACTIONr_scbond_other3.0922.408435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0093.52646
X-RAY DIFFRACTIONr_long_range_B_refined4.92818.351953
X-RAY DIFFRACTIONr_long_range_B_other4.90918.135933
X-RAY DIFFRACTIONr_rigid_bond_restr2.3431582
X-RAY DIFFRACTIONr_sphericity_free33.173524
X-RAY DIFFRACTIONr_sphericity_bonded13.91451600
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 96 -
Rwork0.234 1684 -
obs--100 %

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