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

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Basic information

Entry
Database: PDB / ID: 3twt
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human MCL1 (chimeric peptide)
Components
  • Tankyrase-2
  • human MCL1
KeywordsSIGNALING PROTEIN/PEPTIDE / ankyrin repeat / protein-protein interaction / poly(ADP-ribosyl)ation / substrate recruitment / SIGNALING PROTEIN-PEPTIDE complex
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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 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 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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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
C: Tankyrase-2
D: Tankyrase-2
E: human MCL1
F: human MCL1
G: human MCL1
H: human MCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,89425
Polymers78,7338
Non-polymers2,16017
Water7,188399
1
A: Tankyrase-2
E: human MCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,56610
Polymers19,6832
Non-polymers8838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
F: human MCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9385
Polymers19,6832
Non-polymers2543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
G: human MCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4865
Polymers19,6832
Non-polymers8033
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
H: human MCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9045
Polymers19,6832
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.413, 104.943, 127.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#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: 17851.180 Da / Num. of mol.: 4 / Fragment: UNP residues 488-655
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: Protein/peptide
human MCL1


Mass: 1832.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 416 molecules

#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES-NaOH pH 6.0, 2% (v/v) PEG 400, 2.5 M (NH4)2SO4, 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 17, 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: 1.85→50 Å / Num. all: 70981 / Num. obs: 70981 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.6 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
REFMACrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→40.164 Å / SU ML: 0.55 / σ(F): 0.09 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 3548 5.02 %
Rwork0.1843 --
obs0.186 70721 97.68 %
all-70720 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.795 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0694 Å20 Å20 Å2
2--0.0362 Å2-0 Å2
3---1.0332 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5291 0 116 399 5806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075506
X-RAY DIFFRACTIONf_angle_d17416
X-RAY DIFFRACTIONf_dihedral_angle_d13.6432068
X-RAY DIFFRACTIONf_chiral_restr0.069817
X-RAY DIFFRACTIONf_plane_restr0.006969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87550.29441180.27742258X-RAY DIFFRACTION84
1.8755-1.90220.3231350.27992369X-RAY DIFFRACTION87
1.9022-1.93060.27741330.26342440X-RAY DIFFRACTION91
1.9306-1.96080.27161620.22792504X-RAY DIFFRACTION93
1.9608-1.9930.22611310.21072590X-RAY DIFFRACTION95
1.993-2.02730.25341310.19412679X-RAY DIFFRACTION98
2.0273-2.06420.21931570.18762704X-RAY DIFFRACTION99
2.0642-2.10390.20111290.18082717X-RAY DIFFRACTION100
2.1039-2.14680.21411350.17382735X-RAY DIFFRACTION100
2.1468-2.19350.19441550.17592688X-RAY DIFFRACTION100
2.1935-2.24450.25261530.16842711X-RAY DIFFRACTION100
2.2445-2.30060.20091360.17022734X-RAY DIFFRACTION100
2.3006-2.36280.21221400.16142721X-RAY DIFFRACTION100
2.3628-2.43240.20681540.16162720X-RAY DIFFRACTION100
2.4324-2.51090.20391470.16262736X-RAY DIFFRACTION100
2.5109-2.60060.21041420.1632737X-RAY DIFFRACTION100
2.6006-2.70470.22231580.16332718X-RAY DIFFRACTION100
2.7047-2.82780.20931460.1772750X-RAY DIFFRACTION100
2.8278-2.97680.20211360.182756X-RAY DIFFRACTION100
2.9768-3.16320.21811470.17652746X-RAY DIFFRACTION100
3.1632-3.40730.22171330.17762779X-RAY DIFFRACTION100
3.4073-3.750.17931420.16862783X-RAY DIFFRACTION100
3.75-4.29210.20521420.1652801X-RAY DIFFRACTION100
4.2921-5.40550.21171370.17852842X-RAY DIFFRACTION100
5.4055-40.1730.26181490.24662955X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.41890.43262.41272.90050.44486.3361-0.3679-0.05020.59020.14890.21581.2231-0.7065-0.82290.11650.2110.0857-0.00890.38230.07270.3185-28.2825-10.969711.6628
28.0814.8525-0.14953.9947-2.3976.3402-0.17930.80160.3648-1.55870.55440.97570.1041-0.2363-0.2970.3107-0.0186-0.05980.31440.06140.2584-23.5929-14.20542.8938
35.37714.2719-5.65753.6903-4.25986.13650.3617-0.17110.8084-0.27940.38680.7304-0.4719-0.2703-0.65460.25210.01580.03410.27570.01530.2969-19.5318-7.175213.3776
42.48710.5219-0.74474.90971.95865.4233-0.0126-0.23180.3130.1917-0.00750.5437-0.1807-0.38590.00870.09930.05070.04790.2550.01690.1654-23.3887-16.8417.8759
57.37695.72460.534.5576-0.12812.511-0.32080.8104-0.1717-0.59260.5397-0.43540.08630.0247-0.18820.1714-0.00770.04040.26420.00170.1367-15.1189-18.60247.3273
60.76080.43141.08034.43170.32531.7025-0.0251-0.0630.01240.17080.02680.12650.046-0.16160.0150.09530.00560.04560.2482-0.0050.1217-16.4304-19.193321.1779
74.27863.6128-0.87733.1662-1.03590.94970.00360.314-0.2812-0.49920.0787-0.4850.16840.3192-0.08950.18890.03710.05280.2083-0.0080.1418-10.123-26.494114.3299
81.5246-0.2267-0.16324.05321.15382.3328-0.0905-0.10670.00970.49080.1194-0.11190.46550.0152-0.02620.18260.00650.00090.18110.01350.087-11.9087-27.680526.0903
94.340.7924-2.86811.92040.5045.7750.0814-0.69570.10640.71850.06230.02360.20260.3569-0.21010.426-0.0127-0.01190.3152-0.01130.1462-11.4902-27.61136.5439
100.3069-0.2911-0.35880.38440.54720.814-0.0606-0.1836-0.20960.33060.15410.15660.7305-0.2799-0.24080.8547-0.00450.03040.23890.11570.1179-13.4952-39.921431.8043
114.2075-0.1419-0.25057.27-0.39156.8374-0.0357-0.00570.36290.16710.104-0.2975-0.39050.3124-0.0160.1471-0.0180.00770.1535-0.06010.1583-48.3138-17.229844.471
122.5626-0.2999-1.88182.06311.00982.9975-0.10180.0631-0.0597-0.13030.0397-0.00070.1169-0.0320.05780.1115-0.02050.0030.12770.00770.0818-43.8045-32.846629.3717
132.6922-2.5302-0.28892.66450.75590.84670.14830.09180.560.3346-0.0047-0.2122-0.32820.3234-0.03260.5018-0.08610.220.24430.03490.40539.126811.49887.6019
141.73571.056-0.84893.7263-0.9265.34560.13650.29150.0423-0.51820.0892-0.3532-0.22570.2295-0.0790.3295-0.01080.18270.18890.0140.29551.60358.60739.7403
153.7808-0.48051.89654.1105-0.93845.33020.0210.1338-0.1559-0.46750.0380.0365-0.0711-0.2278-0.03130.2683-0.00170.13150.12970.02180.1562-4.56653.413110.9273
160.01180.18310.21934.55972.85775.27930.06440.04090.1103-0.171-0.15610.039-0.2689-0.2760.05580.210.04080.13140.13220.04680.2534-8.29724.092820.7162
170.76950.8250.38281.0569-0.38484.01130.001-0.0203-0.03090.0077-0.0091-0.0583-0.0892-0.08350.02880.170.0490.08380.16230.01730.2119-6.2145-5.702226.8824
187.7743-4.5308-4.52954.7430.75114.3448-0.6017-0.9804-0.26071.21860.56910.0666-0.15570.24340.03250.46090.17160.08990.3110.05130.2457-8.7499-3.521439.0439
191.39610.59741.42893.93453.05645.1197-0.12190.14530.0941-0.3045-0.0296-0.0525-0.47390.13520.1160.2206-0.0177-0.06680.17350.05130.2038-27.6856-33.0075-10.0354
204.16560.22742.03693.01020.47483.3602-0.03880.0694-0.1007-0.2855-0.00020.18470.0058-0.00820.02270.1573-0.0121-0.06520.13540.05650.1378-26.9136-39.2565-3.4019
211.9758-0.64030.85393.04120.10521.80370.0614-0.0156-0.1662-0.04970.04810.09640.20770.0115-0.10780.1625-0.0018-0.0150.14110.04030.0987-18.1634-48.84667.3848
220.3842-0.69770.0062.15281.48622.54870.0292-0.20670.06680.55990.315-0.58220.35170.63220.02210.29790.1359-0.18140.3278-0.04340.2301-5.6027-49.838516.6004
233.144-0.61851.15135.69734.49717.24130.0222-0.28830.06440.465-0.22140.58770.4721-0.68950.24310.1331-0.05740.06380.20520.02220.2364-25.9713-26.357222.1729
248.59060.8731-1.35337.1572-1.01515.04630.2032-0.31370.11680.1884-0.0933-0.48910.04290.7918-0.07380.1713-0.0185-0.02640.1906-0.05020.1249-38.118-33.090339.7422
251.0573-1.95680.77687.2288-0.11541.11910.1016-0.24930.0772-0.0073-0.0462-0.81840.16490.2694-0.05380.22060.03770.08440.28540.04790.46545.25872.55225.5314
262.666-1.7038-1.71478.87086.09755.0002-0.19660.1115-0.180.02340.3499-0.58590.28740.761-0.1270.26830.07310.02670.33190.00010.1268-10.9831-43.0384-0.9823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 489:502)
2X-RAY DIFFRACTION2chain 'A' and (resseq 503:511)
3X-RAY DIFFRACTION3chain 'A' and (resseq 512:521)
4X-RAY DIFFRACTION4chain 'A' and (resseq 522:538)
5X-RAY DIFFRACTION5chain 'A' and (resseq 539:547)
6X-RAY DIFFRACTION6chain 'A' and (resseq 548:571)
7X-RAY DIFFRACTION7chain 'A' and (resseq 572:580)
8X-RAY DIFFRACTION8chain 'A' and (resseq 581:614)
9X-RAY DIFFRACTION9chain 'A' and (resseq 615:628)
10X-RAY DIFFRACTION10chain 'A' and (resseq 629:644)
11X-RAY DIFFRACTION11chain 'B' and (resseq 488:528)
12X-RAY DIFFRACTION12chain 'B' and (resseq 529:644)
13X-RAY DIFFRACTION13chain 'C' and (resseq 485:502)
14X-RAY DIFFRACTION14chain 'C' and (resseq 503:538)
15X-RAY DIFFRACTION15chain 'C' and (resseq 539:561)
16X-RAY DIFFRACTION16chain 'C' and (resseq 562:580)
17X-RAY DIFFRACTION17chain 'C' and (resseq 581:628)
18X-RAY DIFFRACTION18chain 'C' and (resseq 629:644)
19X-RAY DIFFRACTION19chain 'D' and (resseq 485:511)
20X-RAY DIFFRACTION20chain 'D' and (resseq 512:548)
21X-RAY DIFFRACTION21chain 'D' and (resseq 549:627)
22X-RAY DIFFRACTION22chain 'D' and (resseq 628:644)
23X-RAY DIFFRACTION23chain 'E'
24X-RAY DIFFRACTION24chain 'F'
25X-RAY DIFFRACTION25chain 'G'
26X-RAY DIFFRACTION26chain 'H'

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