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- PDB-5bxu: Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide ... -

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Basic information

Entry
Database: PDB / ID: 5bxu
TitleHuman Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n4m5
Components
  • Tankyrase-2
  • cp4n4m5
KeywordsTRANSFERASE / stapled peptide / protein-protein interaction / ankyrin-repeat domain / tankyrase
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / 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. ...: / Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / 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 / Mainly Alpha
Similarity search - Domain/homology
Chem-4XQ / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsXu, W. / Fischer, G. / Hyvonen, M. / Itzhaki, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1002329 United Kingdom
CitationJournal: to be published
Title: Human Tankyrase-2 in Complex with Extended Stapled Peptide sp4n4m5
Authors: Xu, W. / Lau, Y.H. / Fischer, G. / Chattopadhyay, A. / Tan, Y.S. / Verma, C. / Hyvonen, M. / Spring, D.S. / Itzhaki, L.S.
History
DepositionJun 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / software
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-2
B: cp4n4m5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8924
Polymers18,5662
Non-polymers3262
Water2,810156
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-12 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.086, 63.279, 72.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tankyrase-2 / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 17735.982 Da / Num. of mol.: 1 / Fragment: residues 488-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Plasmid: pGST / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide cp4n4m5


Mass: 829.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-4XQ / 4,4'-pentane-1,5-diylbis(1-propyl-1H-1,2,3-triazole)


Mass: 290.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N6 / Source: (synth.) Homo sapiens (human)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.60 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.75 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.35→28.987 Å / Num. all: 31722 / Num. obs: 31722 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 13.7
Reflection shellResolution: 1.35→1.355 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.711 / % possible all: 92.1

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Processing

Software
NameVersionClassification
Aimless(version 0.3.5)data scaling
XDS(VERSION November 11data reduction
Cootmodel building
REFMAC5.8.0049refinement
PHASERphasing
autoPROCdata reduction
CCP46.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TWQ

3twq


Resolution: 1.35→28.9 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.151 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18634 1557 4.9 %RANDOM
Rwork0.15619 ---
obs0.15768 30126 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å2-0 Å2
2--1.14 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 1 156 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191447
X-RAY DIFFRACTIONr_bond_other_d0.0020.021377
X-RAY DIFFRACTIONr_angle_refined_deg2.1461.9691961
X-RAY DIFFRACTIONr_angle_other_deg1.03733164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.875187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.5492568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30515236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.378158
X-RAY DIFFRACTIONr_chiral_restr0.140.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021755
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02331
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_it1.4811.248731
X-RAY DIFFRACTIONr_mcbond_other1.4741.245729
X-RAY DIFFRACTIONr_mcangle_it2.0791.867924
X-RAY DIFFRACTIONr_mcangle_other2.0781.868925
X-RAY DIFFRACTIONr_scbond_it2.7081.598716
X-RAY DIFFRACTIONr_scbond_other2.7061.599717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9932.281038
X-RAY DIFFRACTIONr_long_range_B_refined5.68111.7441833
X-RAY DIFFRACTIONr_long_range_B_other5.6811.7511834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 96 -
Rwork0.287 2194 -
obs--98.41 %

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