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- PDB-3utm: Crystal structure of a mouse Tankyrase-Axin complex -

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Basic information

Entry
Database: PDB / ID: 3utm
TitleCrystal structure of a mouse Tankyrase-Axin complex
Components
  • Axin-1
  • Tankyrase-1
KeywordsTRANSFERASE/SIGNALING PROTEIN / Tankyrase / TNKS / ankryin repeat clusters / Wnt signaling / poly-ADP-ribosylation / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


beta-catenin destruction complex assembly / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of AXIN / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / head development / Degradation of beta-catenin by the destruction complex / axial mesoderm formation ...beta-catenin destruction complex assembly / Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of AXIN / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / Regulation of PTEN stability and activity / head development / Degradation of beta-catenin by the destruction complex / axial mesoderm formation / dorsal/ventral axis specification / cellular response to nutrient / post-anal tail morphogenesis / beta-catenin destruction complex / Ub-specific processing proteases / positive regulation of telomere capping / epigenetic programming in the zygotic pronuclei / axial mesoderm development / I-SMAD binding / dorsal/ventral pattern formation / positive regulation of ubiquitin-dependent protein catabolic process / Wnt signalosome / regulation of canonical Wnt signaling pathway / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / nucleocytoplasmic transport / negative regulation of protein metabolic process / 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 / negative regulation of fat cell differentiation / mitotic spindle pole / positive regulation of transforming growth factor beta receptor signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / negative regulation of Wnt signaling pathway / R-SMAD binding / negative regulation of transcription elongation by RNA polymerase II / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of protein kinase activity / mRNA transport / lateral plasma membrane / canonical Wnt signaling pathway / ubiquitin-like ligase-substrate adaptor activity / nuclear pore / signaling adaptor activity / protein serine/threonine kinase binding / cytoplasmic microtubule organization / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / positive regulation of protein ubiquitination / positive regulation of JNK cascade / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / protein catabolic process / beta-catenin binding / Wnt signaling pathway / protein polyubiquitination / p53 binding / positive regulation of canonical Wnt signaling pathway / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / cell cortex / cytoplasmic vesicle / nuclear membrane / histone binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / nuclear body / protein domain specific binding / Golgi membrane / cell division / negative regulation of gene expression / apoptotic process / centrosome / ubiquitin protein ligase binding / protein kinase binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Ankyrin repeat-containing domain / 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 / 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 / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Axin-1 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCheng, Z. / Morrone, S. / Xu, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of a Tankyrase-Axin complex and its implications for Axin turnover and Tankyrase substrate recruitment.
Authors: Morrone, S. / Cheng, Z. / Moon, R.T. / Cong, F. / Xu, W.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Axin-1


Theoretical massNumber of molelcules
Total (without water)85,2563
Polymers85,2563
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-52 kcal/mol
Surface area29850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.672, 106.543, 73.428
Angle α, β, γ (deg.)90.00, 105.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tankyrase-1 / TANK1 / TRF1-interacting ankyrin-related ADP-ribose polymerase 1 / Tankyrase I


Mass: 38235.715 Da / Num. of mol.: 2 / Fragment: mTNKS1 ARC23 (UNP Residues 308-655)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TANKRYASE1, Tnks, Tnks1 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6PFX9, NAD+ ADP-ribosyltransferase
#2: Protein Axin-1 / Axis inhibition protein 1 / Protein Fused


Mass: 8784.486 Da / Num. of mol.: 1 / Fragment: mAxin1 N domain (UNP Residues 1-80)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Axin, Axin1, Fu / Plasmid: pAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O35625
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.6
Details: 0.06 M sodium citrate tribasic dihydrate pH 5.6, 1.2M ammonium acetate, 18% MPD, and 20mM DTT, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 70985 / Num. obs: 70726 / % possible obs: 99.85 % / Redundancy: 6.9 % / Rsym value: 0.059 / Net I/σ(I): 30
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.66

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YMP

1ymp


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.628 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23847 3293 5 %RANDOM
Rwork0.20709 ---
obs0.2087 62479 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.174 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-1.84 Å2
2--1.51 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5036 0 0 227 5263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9686937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21224.529223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.415902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8751529
X-RAY DIFFRACTIONr_chiral_restr0.0870.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213831
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 229 -
Rwork0.303 4534 -
obs--99.75 %
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)
10.479-0.36590.43310.3235-0.42340.64550.0186-0.07660.012-0.03130.041-0.00030.0287-0.0822-0.05960.05620.0266-0.01390.05380.02780.065958.679837.4194-33.6585
20.05460.07230.05380.130.19390.5049-0.0075-0.0025-0.0003-0.0150.00520.008-0.00510.04340.00230.03890.0204-0.04660.0671-0.05010.073766.364137.1305-23.0877
30.019-0.0441-0.11330.1760.14160.94270.06130.02230.0046-0.1358-0.2523-0.096-0.76880.12450.1910.6318-0.0778-0.15130.39750.17250.292462.483865.8117-25.0748
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A316 - 635
2X-RAY DIFFRACTION2B328 - 634
3X-RAY DIFFRACTION3C18 - 78

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