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- PDB-6urq: Complex structure of human poly-ADP-ribosyltransferase TNKS1 ARC2... -

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Basic information

Entry
Database: PDB / ID: 6urq
TitleComplex structure of human poly-ADP-ribosyltransferase TNKS1 ARC2-ARC3 and P antigen family member 4 (PAGE4)
Components
  • P antigen family member 4
  • Poly [ADP-ribose] polymerase tankyrase-1
KeywordsTransferase/Transcription / TNKS / PAGE4 / tankyrase / PARP / cancer-testis antigen / Wnt signaling / Transferase-Transcription complex
Function / homology
Function and homology information


negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / regulation of stress-activated MAPK cascade / protein poly-ADP-ribosylation ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / regulation of stress-activated MAPK cascade / protein poly-ADP-ribosylation / pericentriolar material / response to starvation / mitotic spindle pole / : / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / spindle assembly / nuclear pore / negative regulation of reactive oxygen species biosynthetic process / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / peptidyl-threonine phosphorylation / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / peptidyl-serine phosphorylation / nuclear membrane / nucleic acid binding / chromosome, telomeric region / transcription coactivator activity / nuclear body / intracellular signal transduction / Ub-specific processing proteases / Golgi membrane / cell division / negative regulation of apoptotic process / Golgi apparatus / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
GAGE family / GAGE / GAGE protein / GAGE / : / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. ...GAGE family / GAGE / GAGE protein / GAGE / : / 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
Similarity search - Domain/homology
P antigen family member 4 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZheng, Y. / Koirala, S. / Miller, D. / Potts, P.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP140661 United States
CitationJournal: Cell Rep / Year: 2020
Title: Tissue-Specific Regulation of the Wnt/ beta-Catenin Pathway by PAGE4 Inhibition of Tankyrase.
Authors: Koirala, S. / Klein, J. / Zheng, Y. / Glenn, N.O. / Eisemann, T. / Fon Tacer, K. / Miller, D.J. / Kulak, O. / Lu, M. / Finkelstein, D.B. / Neale, G. / Tillman, H. / Vogel, P. / Strand, D.W. ...Authors: Koirala, S. / Klein, J. / Zheng, Y. / Glenn, N.O. / Eisemann, T. / Fon Tacer, K. / Miller, D.J. / Kulak, O. / Lu, M. / Finkelstein, D.B. / Neale, G. / Tillman, H. / Vogel, P. / Strand, D.W. / Lum, L. / Brautigam, C.A. / Pascal, J.M. / Clements, W.K. / Potts, P.R.
History
DepositionOct 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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: Poly [ADP-ribose] polymerase tankyrase-1
B: Poly [ADP-ribose] polymerase tankyrase-1
C: P antigen family member 4
D: P antigen family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4256
Polymers92,2364
Non-polymers1882
Water5,981332
1
A: Poly [ADP-ribose] polymerase tankyrase-1
D: P antigen family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2143
Polymers46,1182
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase tankyrase-1
C: P antigen family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2103
Polymers46,1182
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.908, 101.035, 75.418
Angle α, β, γ (deg.)90.000, 107.232, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Poly [ADP-ribose] polymerase tankyrase-1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / Protein ...ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / Protein poly-ADP-ribosyltransferase tankyrase-1 / TNKS-1 / TRF1-interacting ankyrin-related ADP-ribose polymerase / Tankyrase I / Tankyrase-1 / TANK1


Mass: 34948.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95271, NAD+ ADP-ribosyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein P antigen family member 4 / PAGE-4 / G antigen family C member 1 / PAGE-1


Mass: 11170.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAGE4, GAGEC1, JM27 / Production host: Escherichia coli (E. coli) / References: UniProt: O60829
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 100 mM Ammonium Sulfate, 10 mM DTT, 100 mM MES pH 6.0, 7% w/v PEG4000, 1% 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→39.75 Å / Num. obs: 60143 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.24 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.043 / Rrim(I) all: 0.085 / Rsym value: 0.073 / Net I/σ(I): 10.2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4432 / Rpim(I) all: 0.422 / Rrim(I) all: 0.834 / Rsym value: 0.718 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHASER(1.14_3260: ???)phasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTM

3utm


Resolution: 2.05→39.75 Å / SU ML: 0.2466 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 26.0844
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2463 2997 4.99 %
Rwork0.2042 57115 -
obs0.2062 60112 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.14 Å2
Refinement stepCycle: LAST / Resolution: 2.05→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 11 332 5100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714862
X-RAY DIFFRACTIONf_angle_d0.8226588
X-RAY DIFFRACTIONf_chiral_restr0.0452764
X-RAY DIFFRACTIONf_plane_restr0.0053862
X-RAY DIFFRACTIONf_dihedral_angle_d15.02221767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.080.32261370.28432664X-RAY DIFFRACTION98.38
2.08-2.120.33661400.27292701X-RAY DIFFRACTION98.51
2.12-2.160.28671460.26472708X-RAY DIFFRACTION98.65
2.16-2.20.33051470.26422691X-RAY DIFFRACTION98.75
2.2-2.240.29771450.24382692X-RAY DIFFRACTION98.78
2.24-2.290.32221390.24082695X-RAY DIFFRACTION98.85
2.29-2.350.2611440.23192685X-RAY DIFFRACTION98.95
2.35-2.410.28721540.23162723X-RAY DIFFRACTION99.14
2.41-2.470.31390.22592706X-RAY DIFFRACTION99.03
2.47-2.540.24731350.22372691X-RAY DIFFRACTION99.16
2.54-2.630.30611510.20742721X-RAY DIFFRACTION99.21
2.63-2.720.23371420.21072718X-RAY DIFFRACTION99.37
2.72-2.830.23191490.21372693X-RAY DIFFRACTION99.34
2.83-2.960.22641380.21522722X-RAY DIFFRACTION99.51
2.96-3.110.26121420.21932748X-RAY DIFFRACTION99.55
3.11-3.310.29011550.22112725X-RAY DIFFRACTION99.69
3.31-3.560.2621180.1972756X-RAY DIFFRACTION99.69
3.56-3.920.21551580.18542725X-RAY DIFFRACTION99.83
3.92-4.490.2111530.16662764X-RAY DIFFRACTION99.79
4.49-5.650.20681310.18432762X-RAY DIFFRACTION99.86
5.65-39.750.20531340.17942825X-RAY DIFFRACTION99.7

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