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- PDB-5hkp: Crystal structure of mouse Tankyrase/human TRF1 complex -

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Basic information

Entry
Database: PDB / ID: 5hkp
TitleCrystal structure of mouse Tankyrase/human TRF1 complex
Components
  • Tankyrase-1
  • Telomeric repeat-binding factor 1
KeywordsTRANSFERASE / SIGNALING PROTEIN / Tankyrase / TRF1 / telomere / TRANSFERASE - SIGNALING PROTEIN complex
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / TCF dependent signaling in response to WNT / Degradation of AXIN / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / 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 / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / cellular response to nutrient / Processive synthesis on the C-strand of the telomere / nuclear telomere cap complex / G-rich strand telomeric DNA binding / positive regulation of telomere maintenance / Polymerase switching on the C-strand of the telomere / ankyrin repeat binding / Removal of the Flap Intermediate from the C-strand / Ub-specific processing proteases / telomere capping / negative regulation of telomere maintenance via telomerase / DNA binding, bending / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / telomeric DNA binding / protein poly-ADP-ribosylation / negative regulation of DNA replication / negative regulation of telomerase activity / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Telomere Extension By Telomerase / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / telomere maintenance via telomerase / mRNA transport / nuclear pore / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / positive regulation of telomere maintenance via telomerase / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / nucleotidyltransferase activity / DNA Damage/Telomere Stress Induced Senescence / spindle / fibrillar center / Wnt signaling pathway / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / microtubule binding / nuclear membrane / chromosome, telomeric region / molecular adaptor activity / nuclear body / cell cycle / cell division / Golgi membrane / centrosome / nucleolus / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Ankyrin repeat-containing domain / Myb-like DNA-binding domain / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain ...Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Ankyrin repeat-containing domain / Myb-like DNA-binding 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) / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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 / Homeobox-like domain superfamily / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 1 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, Z. / Li, B. / Rao, Z. / Xu, W.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of a tankyrase 1-telomere repeat factor 1 complex.
Authors: Li, B. / Qiao, R. / Wang, Z. / Zhou, W. / Li, X. / Xu, W. / Rao, Z.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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

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Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Telomeric repeat-binding factor 1
D: Telomeric repeat-binding factor 1


Theoretical massNumber of molelcules
Total (without water)88,9294
Polymers88,9294
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-40 kcal/mol
Surface area29220 Å2
Unit cell
Length a, b, c (Å)134.995, 100.069, 75.951
Angle α, β, γ (deg.)90.000, 107.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tankyrase-1 / / TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / TRF1-interacting ankyrin-related ...TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / TRF1-interacting ankyrin-related ADP-ribose polymerase 1 / Tankyrase I


Mass: 38235.715 Da / Num. of mol.: 2 / Fragment: UNP residues 308-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnks, Tnks1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PFX9, NAD+ ADP-ribosyltransferase
#2: Protein Telomeric repeat-binding factor 1 / NIMA-interacting protein 2 / TTAGGG repeat-binding factor 1 / Telomeric protein Pin2/TRF1


Mass: 6228.560 Da / Num. of mol.: 2 / Fragment: UNP residues 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P54274
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.035M Calcium Chloride dihydrate 0.07M MES monohydrate pH6.0 0.03M Tris pH8.5 31.5% v/v Polyethylene glycol 200 6% v/v Ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→79 Å / Num. obs: 48080 / % possible obs: 98.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.111 / Net I/av σ(I): 8.815 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.263.10.397197.7
2.26-2.343.10.32197.9
2.34-2.4230.258198.4
2.42-2.522.90.207198.1
2.52-2.633.10.177198.5
2.63-2.773.20.164198.2
2.77-2.953.20.15198.8
2.95-3.173.10.13199.2
3.17-3.493.10.119199.3
3.49-43.30.114199.7
4-5.0430.101199.4
5.04-503.30.094199.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTM

3utm


Resolution: 2.2→79 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.011 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2425 5 %RANDOM
Rwork0.1984 ---
obs0.1999 45650 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.41 Å2 / Biso mean: 53.319 Å2 / Biso min: 31.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-2.93 Å2
2--1.86 Å20 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 2.2→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4943 0 0 106 5049
Biso mean---47.21 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195029
X-RAY DIFFRACTIONr_bond_other_d0.0010.024928
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9636796
X-RAY DIFFRACTIONr_angle_other_deg0.759311333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4355643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74324.389221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98515888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3911530
X-RAY DIFFRACTIONr_chiral_restr0.0690.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215721
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021121
X-RAY DIFFRACTIONr_mcbond_it1.6573.0922584
X-RAY DIFFRACTIONr_mcbond_other1.6573.092583
X-RAY DIFFRACTIONr_mcangle_it2.5884.6213223
LS refinement shellResolution: 2.196→2.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 150 -
Rwork0.28 2946 -
all-3096 -
obs--85.36 %
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)
11.3684-1.09060.9071.1815-1.16652.0932-0.0326-0.15120.02770.03170.14430.0369-0.1873-0.3227-0.11170.03670.00220.01850.2469-0.01780.1131-16.9832-13.96682.2036
20.2770.36940.21630.74620.98492.1729-0.0028-0.03460.0089-0.02380.0061-0.0289-0.08270.0359-0.00320.01190.041-0.0140.25810.00330.1808-9.9606-13.272512.6945
34.78665.2517-5.13517.2843-2.724611.07010.4528-0.2751-0.1137-0.0792-1.01050.1013-1.5739-1.06780.55770.25810.2441-0.09360.3533-0.09640.0386-32.497412.0646-7.0642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A322 - 634
2X-RAY DIFFRACTION2B324 - 634
3X-RAY DIFFRACTION3C11 - 22

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