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- PDB-6cf6: RNF146 TBM-Tankyrase ARC2-3 complex -

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Basic information

Entry
Database: PDB / ID: 6cf6
TitleRNF146 TBM-Tankyrase ARC2-3 complex
Components
  • RNF146
  • Tankyrase-1
KeywordsPROTEIN BINDING / complex / E3 ligase / PARP / ankyrin repeat
Function / homology
Function and homology information


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 / poly-ADP-D-ribose binding / cellular response to nutrient / Ub-specific processing proteases / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation ...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 / poly-ADP-D-ribose binding / cellular response to nutrient / Ub-specific processing proteases / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / mRNA transport / protein autoubiquitination / protein K48-linked ubiquitination / nuclear pore / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / RING-type E3 ubiquitin transferase / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / protein transport / histone binding / ubiquitin-dependent protein catabolic process / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell cycle / cell division / Golgi membrane / centrosome / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF146 / RNF146, RING finger, HC subclass / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Ankyrin repeats (many copies) / Zinc finger, C3HC4 type (RING finger) ...E3 ubiquitin-protein ligase RNF146 / RNF146, RING finger, HC subclass / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Ankyrin repeats (many copies) / Zinc finger, C3HC4 type (RING finger) / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ring finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase tankyrase-1 / E3 ubiquitin-protein ligase RNF146
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsDa Rosa, P.A. / Xu, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007270 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM099766 United States
CitationJournal: Protein Sci. / Year: 2018
Title: Structural basis for tankyrase-RNF146 interaction reveals noncanonical tankyrase-binding motifs.
Authors: DaRosa, P.A. / Klevit, R.E. / Xu, W.
History
DepositionFeb 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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: Tankyrase-1
B: Tankyrase-1
C: RNF146
D: RNF146


Theoretical massNumber of molelcules
Total (without water)78,3914
Polymers78,3914
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry, Affinity of 5.8 micromolar
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.019, 103.284, 75.163
Angle α, β, γ (deg.)90.000, 106.930, 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: 37902.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnks, Tnks1 / Variant: Tankyrase 1 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PFX9, NAD+ ADP-ribosyltransferase
#2: Protein/peptide RNF146 /


Mass: 1293.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NTX7*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30 mM sodium citrate pH 5.6, 60 mM ammonium acetate, 27% 2-methyl-2,4-pentanediol
PH range: 5.6-8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2014
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 71212 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.063 / Χ2: 1.022 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-1.992.30.46545260.7750.3440.5820.93974.3
1.99-2.052.90.43756650.8280.2950.531.03393.2
2.05-2.123.40.36760270.9010.2310.4351.11299.1
2.12-2.213.70.29860980.9420.1790.3481.099100
2.21-2.313.80.2160550.9680.1250.2441.095100
2.31-2.433.80.14760910.9830.0870.1711.04100
2.43-2.583.80.10560900.9920.0620.1221.057100
2.58-2.783.80.07461070.9950.0440.0860.999100
2.78-3.063.80.05360810.9970.0310.0620.941100
3.06-3.513.80.04661430.9970.0270.0540.941100
3.51-4.423.70.04361410.9970.0260.0510.969100
4.42-503.70.02561880.9990.0150.030.99999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTM

3utm


Resolution: 1.93→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.19 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 3512 4.9 %RANDOM
Rwork0.1954 ---
obs0.197 67700 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.12 Å2 / Biso mean: 38.986 Å2 / Biso min: 19.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.83 Å2
2--2.3 Å20 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 0 295 5325
Biso mean---41.93 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195132
X-RAY DIFFRACTIONr_bond_other_d0.0020.024825
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9626941
X-RAY DIFFRACTIONr_angle_other_deg0.956311219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5185661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70424.574223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0515903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3131528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02940
LS refinement shellResolution: 1.931→1.981 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 194 -
Rwork0.301 3702 -
all-3896 -
obs--71.82 %
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)
10.7997-0.69010.76780.7231-0.78411.0641-0.0531-0.19060.01940.01470.12230.0038-0.043-0.2391-0.06920.02950.0275-0.02770.1040.02790.074660.541738.7408-34.6706
20.15510.18490.12590.41020.57851.3788-0.0291-0.0539-0.0491-0.06910.0314-0.0103-0.07760.096-0.00220.03270.0127-0.03980.13210.00860.103668.743439.4109-22.17
37.0751-2.18750.1772.11291.27731.7243-0.14511.49740.7642-0.251-0.22560.1758-0.70190.35830.37080.4338-0.1649-0.07130.45870.23280.204674.898665.3898-11.5286
45.33677.52820.31610.64670.42354.54920.1546-0.48240.1770.2488-0.64750.1847-0.9606-0.64130.49290.3030.1803-0.12280.1695-0.10120.264748.608565.8491-43.5071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A315 - 634
2X-RAY DIFFRACTION2B316 - 634
3X-RAY DIFFRACTION3C191 - 202
4X-RAY DIFFRACTION4D192 - 201

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