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- PDB-3twq: Crystal structure of ARC4 from human Tankyrase 2 (apo form) -

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Basic information

Entry
Database: PDB / ID: 3twq
TitleCrystal structure of ARC4 from human Tankyrase 2 (apo form)
ComponentsTankyrase-2
KeywordsSIGNALING PROTEIN / ankyrin repeat / protein-protein interaction / poly(ADP-ribosyl)ation / substrate recruitment
Function / homology
Function and homology information


XAV939 stabilizes AXIN / 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 / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases ...XAV939 stabilizes AXIN / 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 / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Ankyrin repeat-containing 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) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Ankyrin repeat / Ankyrin repeat-containing 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) / 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
Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3659
Polymers37,7012
Non-polymers6657
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-70 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.524, 47.524, 250.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-156-

HOH

21B-133-

HOH

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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: 18850.391 Da / Num. of mol.: 2 / Fragment: UNP residues 484-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M HEPES-NaOH pH 8.0, 0.2 M Li2SO4, 35% PEG 3350, 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: Jul 18, 2010
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: 2.15→50 Å / Num. all: 17759 / Num. obs: 17759 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2 / % possible all: 96.9

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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: 2.151→36.929 Å / SU ML: 0.56 / σ(F): 0.5 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 905 5.13 %
Rwork0.1736 --
obs0.1767 17647 97.01 %
all-17647 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.763 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3851 Å2-0 Å20 Å2
2---0.3851 Å2-0 Å2
3---0.7701 Å2
Refinement stepCycle: LAST / Resolution: 2.151→36.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 37 157 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072568
X-RAY DIFFRACTIONf_angle_d1.0463474
X-RAY DIFFRACTIONf_dihedral_angle_d13.187934
X-RAY DIFFRACTIONf_chiral_restr0.07390
X-RAY DIFFRACTIONf_plane_restr0.005450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.151-2.28610.28341460.22292750X-RAY DIFFRACTION97
2.2861-2.46250.27171600.192733X-RAY DIFFRACTION97
2.4625-2.71030.25251550.17252746X-RAY DIFFRACTION97
2.7103-3.10230.23091460.17842793X-RAY DIFFRACTION97
3.1023-3.90790.21181490.15212846X-RAY DIFFRACTION98
3.9079-36.93410.2131490.16792874X-RAY DIFFRACTION96
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)
10.3658-1.50290.70896.8191-2.97441.6172-0.18290.17010.05790.01390.31090.17540.027-0.3086-0.13180.1108-0.03520.00530.20410.01220.11794.3883-11.048814.0414
21.37630.7507-0.88232.3726-0.40431.2297-0.17440.1484-0.0784-0.7830.255-0.4982-0.02820.158-0.04590.196-0.04740.06190.1167-0.02820.119611.4338-19.375116.401
32.29521.1591-0.98354.36480.43211.82710.01630.09170.1647-0.09790.07190.23950.0409-0.207-0.00460.10570.01140.01690.08410.0150.0865.8807-14.572825.4311
41.67781.0929-0.18912.47790.22961.9076-0.0382-0.0026-0.16670.03430.0044-0.05850.04850.03-0.01720.1004-0.01330.00370.08750.01370.072712.2437-16.018329.3958
56.07831.8873-1.95464.5295-3.70268.72960.1696-0.304-0.67240.0893-0.0869-0.25270.30560.52120.13390.25850.0666-0.03510.12110.04090.11216.168-22.207736.0329
64.7038-1.37530.42411.4552-1.00321.0544-0.03040.3396-0.1078-0.0214-0.1102-0.00350.04090.10880.04950.0485-0.1221-0.03970.1336-0.03060.132212.9743-6.903337.5316
74.44321.206-1.83096.17260.19984.7226-0.1547-0.1688-0.2598-0.10390.14830.06650.3105-0.105-0.00630.09860.0062-0.00870.103-0.00140.058711.978-16.745445.1291
83.2868-1.3639-0.34143.8197-0.23410.82-0.0563-0.3992-0.07210.21970.04160.08910.13370.06390.02010.10230.014-0.00880.12890.00540.07639.0743-9.640751.467
96.84111.6047-2.44550.426-0.46171.12030.0915-0.06090.46260.09450.01560.1431-0.07090.0129-0.10080.1587-0.00730.00390.0795-0.0260.087812.57484.098528.2241
102.36971.21610.79942.11310.02752.88960.1865-0.0921-0.05470.0518-0.1238-0.00610.0822-0.0359-0.06660.0856-0.00720.00480.07420.00890.085420.95751.158419.7906
112.4430.27031.27017.091-1.99685.03120.01730.1164-0.1898-0.2180.1102-0.36210.01530.3725-0.05250.065-0.0089-0.00010.1411-0.00280.050924.49020.55637.3457
121.5066-0.37180.10971.7278-0.83363.04780.02880.2245-0.0119-0.2128-0.0727-0.19070.28770.3371-0.00150.16640.0282-0.00370.1174-0.02870.102217.1888-2.6229-4.1574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 481:502)
2X-RAY DIFFRACTION2chain 'A' and (resseq 503:521)
3X-RAY DIFFRACTION3chain 'A' and (resseq 522:538)
4X-RAY DIFFRACTION4chain 'A' and (resseq 539:571)
5X-RAY DIFFRACTION5chain 'A' and (resseq 572:580)
6X-RAY DIFFRACTION6chain 'A' and (resseq 581:594)
7X-RAY DIFFRACTION7chain 'A' and (resseq 595:614)
8X-RAY DIFFRACTION8chain 'A' and (resseq 615:644)
9X-RAY DIFFRACTION9chain 'B' and (resseq 481:502)
10X-RAY DIFFRACTION10chain 'B' and (resseq 503:561)
11X-RAY DIFFRACTION11chain 'B' and (resseq 562:581)
12X-RAY DIFFRACTION12chain 'B' and (resseq 582:644)

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