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- PDB-5gp7: Structural basis for the binding between Tankyrase-1 and USP25 -

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Basic information

Entry
Database: PDB / ID: 5gp7
TitleStructural basis for the binding between Tankyrase-1 and USP25
Components
  • Tankyrase-1
  • Ubiquitin carboxyl-terminal hydrolase 25
KeywordsTRANSFERASE / Tankyrase / USP25 / Ankyrin repeats
Function / homology
Function and homology information


negative regulation of interleukin-17-mediated signaling pathway / ubiquitin-like protein peptidase activity / : / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / negative regulation of ERAD pathway / positive regulation of telomere maintenance via telomere lengthening / regulation of telomere maintenance via telomerase / SUMO binding / deubiquitinase activity / protein K48-linked deubiquitination ...negative regulation of interleukin-17-mediated signaling pathway / ubiquitin-like protein peptidase activity / : / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / negative regulation of ERAD pathway / positive regulation of telomere maintenance via telomere lengthening / regulation of telomere maintenance via telomerase / SUMO binding / deubiquitinase activity / protein K48-linked deubiquitination / XAV939 stabilizes AXIN / positive regulation of telomere capping / protein K63-linked deubiquitination / NAD+ ADP-ribosyltransferase / negative regulation of response to oxidative stress / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / pericentriolar material / mitotic spindle pole / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / protein deubiquitination / mRNA transport / nuclear pore / spindle assembly / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / peptidyl-threonine phosphorylation / ubiquitin binding / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / regulation of protein stability / protein modification process / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / peptidase activity / peptidyl-serine phosphorylation / ATPase binding / nuclear membrane / histone binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / chromosome, telomeric region / Ub-specific processing proteases / nuclear body / Golgi membrane / cell division / ubiquitin protein ligase binding / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / Ankyrin repeats (many copies) / Ubiquitin-interacting motif. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site ...: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / Ankyrin repeats (many copies) / Ubiquitin-interacting motif. / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ankyrin repeat-containing domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / UBA-like superfamily / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Papain-like cysteine peptidase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase tankyrase-1 / Ubiquitin carboxyl-terminal hydrolase 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsLiu, J. / Xu, D. / Fu, T. / Pan, L.
CitationJournal: Genes Dev. / Year: 2017
Title: USP25 regulates Wnt signaling by controlling the stability of tankyrases
Authors: Xu, D. / Liu, J. / Fu, T. / Shan, B. / Qian, L. / Pan, L. / Yuan, J.
History
DepositionAug 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 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: Tankyrase-1
B: Ubiquitin carboxyl-terminal hydrolase 25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3954
Polymers19,2112
Non-polymers1842
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-1 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.506, 59.242, 39.995
Angle α, β, γ (deg.)90.00, 100.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tankyrase-1


Mass: 18149.496 Da / Num. of mol.: 1 / Fragment: UNP residues 799-957
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, NAD+ ADP-ribosyltransferase
#2: Protein/peptide Ubiquitin carboxyl-terminal hydrolase 25 / USP25


Mass: 1061.152 Da / Num. of mol.: 1 / Fragment: UNP residues 1046-1055
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHP3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES/sodium hydroxide, 200 mM sodium chloride, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 25690 / % possible obs: 98.72 % / Redundancy: 3.3 % / Net I/σ(I): 10.93
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWU

3twu


Resolution: 1.502→39.303 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.25
RfactorNum. reflection% reflection
Rfree0.2072 2000 7.79 %
Rwork0.1715 --
obs0.1743 25690 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.502→39.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 12 245 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081346
X-RAY DIFFRACTIONf_angle_d0.9561836
X-RAY DIFFRACTIONf_dihedral_angle_d9.453836
X-RAY DIFFRACTIONf_chiral_restr0.058212
X-RAY DIFFRACTIONf_plane_restr0.007245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5025-1.54010.25271310.22071563X-RAY DIFFRACTION91
1.5401-1.58170.23881350.20231599X-RAY DIFFRACTION95
1.5817-1.62820.21761450.19381704X-RAY DIFFRACTION99
1.6282-1.68080.2361420.19581688X-RAY DIFFRACTION100
1.6808-1.74090.24951450.18981710X-RAY DIFFRACTION100
1.7409-1.81060.2131420.18441695X-RAY DIFFRACTION100
1.8106-1.8930.25191440.18491692X-RAY DIFFRACTION99
1.893-1.99280.21061440.1781716X-RAY DIFFRACTION100
1.9928-2.11760.2031450.16181713X-RAY DIFFRACTION100
2.1176-2.28110.20131440.16721699X-RAY DIFFRACTION100
2.2811-2.51060.18941460.16411728X-RAY DIFFRACTION100
2.5106-2.87380.20161430.16581708X-RAY DIFFRACTION100
2.8738-3.62030.20021460.16091725X-RAY DIFFRACTION100
3.6203-39.31610.19011480.16261750X-RAY DIFFRACTION100

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