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

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Basic information

Entry
Database: PDB / ID: 5bxo
TitleHuman Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3
Components(Tankyrase-2) x 2
KeywordsTRANSFERASE / stapled peptide / protein-protein interaction / ankyrin-repeat domain / tankyrase
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / 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 / NAD+-protein mono-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / 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 / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / NAD+ 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 / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / 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 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 / Mainly Alpha
Similarity search - Domain/homology
Chem-4XP / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.334 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 sp4n2m3
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 1.1Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,35315
Polymers37,1304
Non-polymers1,22311
Water4,990277
1
A: Tankyrase-2
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1377
Polymers18,5652
Non-polymers5735
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-33 kcal/mol
Surface area8590 Å2
MethodPISA
2
B: Tankyrase-2
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2168
Polymers18,5652
Non-polymers6516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-34 kcal/mol
Surface area9170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.823, 46.014, 54.472
Angle α, β, γ (deg.)78.45, 88.99, 72.35
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 487 - 645 / Label seq-ID: 2 - 160

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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.: 2 / 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) / Variant (production host): C41 / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide 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: 828.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase

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Non-polymers , 4 types, 288 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-4XP / 4,4'-propane-1,3-diylbis(1-methyl-1H-1,2,3-triazole)


Mass: 206.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N6 / Source: (synth.) Homo sapiens (human)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.61 % / Description: thin needle
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M tri-sodium citrate, pH 5.0, 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91731 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91731 Å / Relative weight: 1
ReflectionResolution: 1.334→53.312 Å / Num. all: 59052 / Num. obs: 59052 / % possible obs: 95.9 % / Observed criterion σ(F): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.101 / Net I/σ(I): 15.2
Reflection shellResolution: 1.334→1.338 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.3 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementResolution: 1.334→53.31 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.157 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20273 2934 5 %RANDOM
Rwork0.17484 ---
obs0.17623 56016 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å2-0.09 Å2
2--0.84 Å20.49 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.334→53.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 42 277 2932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192964
X-RAY DIFFRACTIONr_bond_other_d0.0050.022835
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9794023
X-RAY DIFFRACTIONr_angle_other_deg1.2336538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4025395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.41224.809131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52415507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3651517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023587
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02658
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_it1.2471.4461509
X-RAY DIFFRACTIONr_mcbond_other1.2461.4461510
X-RAY DIFFRACTIONr_mcangle_it1.9762.1511916
X-RAY DIFFRACTIONr_mcangle_other1.9762.1511917
X-RAY DIFFRACTIONr_scbond_it1.7981.7011455
X-RAY DIFFRACTIONr_scbond_other1.7971.7041456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7492.4592105
X-RAY DIFFRACTIONr_long_range_B_refined5.19612.6773680
X-RAY DIFFRACTIONr_long_range_B_other5.19512.6913681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9517 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.334→1.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 188 -
Rwork0.317 3990 -
obs--91.68 %

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