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- PDB-3twu: Crystal structure of ARC4 from human Tankyrase 2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3twu
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human MCL1
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • Tankyrase-2
KeywordsSIGNALING PROTEIN/PEPTIDE / ankyrin repeat / protein-protein interaction / substrate recruitment / poly(ADP-ribosyl)ation / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / XAV939 stabilizes AXIN / positive regulation of telomere capping / cellular homeostasis / NAD+ ADP-ribosyltransferase / mitochondrial fusion / Bcl-2 family protein complex / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / XAV939 stabilizes AXIN / positive regulation of telomere capping / cellular homeostasis / NAD+ ADP-ribosyltransferase / mitochondrial fusion / Bcl-2 family protein complex / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / BH3 domain binding / negative regulation of anoikis / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of telomere maintenance via telomerase / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / nucleotidyltransferase activity / negative regulation of autophagy / release of cytochrome c from mitochondria / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / protein polyubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by ALK fusions and activated point mutants / nuclear envelope / positive regulation of canonical Wnt signaling pathway / positive regulation of neuron apoptotic process / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / chromosome, telomeric region / Ub-specific processing proteases / positive regulation of apoptotic process / protein heterodimerization activity / Golgi membrane / DNA damage response / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / mitochondrion / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / Ankyrin repeat / Ankyrin repeat-containing domain / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family ...Apoptosis regulator, Mcl-1 / Ankyrin repeat / Ankyrin repeat-containing domain / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / 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
Induced myeloid leukemia cell differentiation protein Mcl-1 / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuettler, S. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis and sequence rules for substrate recognition by tankyrase explain the basis for cherubism disease.
Authors: Guettler, S. / Larose, J. / Petsalaki, E. / Gish, G. / Scotter, A. / Pawson, T. / Rottapel, R. / Sicheri, F.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)19,7142
Polymers19,7142
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-3 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.702, 45.759, 95.662
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 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose ...TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 17995.311 Da / Num. of mol.: 1 / Fragment: UNP residues 488-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pETM-30-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 1718.977 Da / Num. of mol.: 1 / Fragment: UNP residues 73-88 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07820
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES-NaOH pH 6.5, 0.2 M NaOAc, 35% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2011
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 14331 / Num. obs: 14331 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.4 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.4 / % possible all: 91.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.831 Å / SU ML: 0.43 / σ(F): 0.54 / Phase error: 18.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 719 5.06 %Random
Rwork0.1821 ---
obs0.1843 14222 96.74 %-
all-14222 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.39 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1928 Å20 Å2-0 Å2
2--1.9436 Å20 Å2
3----2.1364 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 0 109 1425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071340
X-RAY DIFFRACTIONf_angle_d1.0391819
X-RAY DIFFRACTIONf_dihedral_angle_d12.978494
X-RAY DIFFRACTIONf_chiral_restr0.066206
X-RAY DIFFRACTIONf_plane_restr0.006242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.94020.28551320.23412513X-RAY DIFFRACTION92
1.9402-2.13540.23761450.17352675X-RAY DIFFRACTION97
2.1354-2.44440.21971620.16722669X-RAY DIFFRACTION97
2.4444-3.07960.22691360.16592754X-RAY DIFFRACTION98
3.0796-47.84790.2191440.18952892X-RAY DIFFRACTION98
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)
15.8472-1.4876-0.9535.56010.12684.2967-0.1199-0.0598-0.4824-0.39440.3847-0.90090.82691.0204-0.06340.3810.04470.09390.3053-0.16530.279915.4999-3.11370.2054
21.47850.26230.56785.8259-0.18062.60840.0799-0.0535-0.1273-0.2227-0.08120.06530.9124-0.0494-0.04040.3647-0.06160.08990.1994-0.0720.22848.526-5.351.5446
33.0224-0.32030.85063.83890.14676.9017-0.1787-0.198-0.0277-0.24820.1136-0.62160.22710.22330.07280.18490.01050.07160.1462-0.05520.227212.48684.72466.1459
43.17991.61040.91765.31360.53221.6215-00.1952-0.2856-0.0427-0.19280.78240.8419-0.4554-0.11390.3392-0.13290.03250.2251-0.13090.20590.0303-0.22382.4831
50.78-0.95370.09574.1672-0.22954.6059-0.024-0.024-0.034-0.08120.1046-0.20160.17350.0759-0.05750.1004-0.01190.02190.1266-0.03220.14187.84047.781312.4593
61.50940.4619-3.22567.796-2.56467.2239-0.14310.3221-0.257-0.2790.16960.39440.0852-0.9928-0.00990.1273-0.0192-0.030.2261-0.0360.1616-3.36739.41318.0103
73.30512.1379-0.03064.1031-0.04583.0425-0.0349-0.0849-0.3359-0.02730.0321-0.2005-0.00950.1088-0.00430.07090.01350.00850.11510.00330.12146.636210.583619.8174
82.5562-0.8595-1.25534.122-0.49436.4988-0.01990.17860.0207-0.25850.085-0.0907-0.2196-0.0088-0.06460.1296-0.0161-0.00210.0643-0.0370.11810.45519.294713.5875
94.3516-1.43411.22313.2194-0.34112.72130.0385-0.57130.45020.4214-0.0624-0.3820.0410.20630.02010.15940.009-0.0220.1941-0.02850.17756.937819.559425.249
106.6464-1.50563.42758.2778-0.93567.8902-0.23750.52871.0599-0.70380.0594-0.3949-0.87980.72680.13250.1927-0.06570.03980.1365-0.02560.27066.22828.487917.3546
112.4609-1.042-1.44984.50612.27514.83850.1355-0.02180.2269-0.0417-0.30010.5597-0.3919-0.48290.14540.13410.0281-0.0482-0.0209-0.16830.1621-3.804629.243818.2483
125.76862.62393.10132.66841.57584.5117-0.15640.5157-0.3302-0.48980.1277-0.04150.01590.08540.11810.1652-0.00430.03280.2453-0.07550.177412.74614.77667.3273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 489:502)
2X-RAY DIFFRACTION2chain 'A' and (resseq 503:521)
3X-RAY DIFFRACTION3chain 'A' and (resseq 522:538)
4X-RAY DIFFRACTION4chain 'A' and (resseq 539:548)
5X-RAY DIFFRACTION5chain 'A' and (resseq 549:571)
6X-RAY DIFFRACTION6chain 'A' and (resseq 572:580)
7X-RAY DIFFRACTION7chain 'A' and (resseq 581:594)
8X-RAY DIFFRACTION8chain 'A' and (resseq 595:614)
9X-RAY DIFFRACTION9chain 'A' and (resseq 615:627)
10X-RAY DIFFRACTION10chain 'A' and (resseq 628:636)
11X-RAY DIFFRACTION11chain 'A' and (resseq 637:648)
12X-RAY DIFFRACTION12chain 'B'

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