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- PDB-6cvo: Human Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn produc... -

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Basic information

Entry
Database: PDB / ID: 6cvo
TitleHuman Aprataxin (Aptx) bound to nicked RNA-DNA, AMP and Zn product complex
Components
  • Aprataxin
  • DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')
  • DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3')
KeywordsHYDROLASE/DNA/RNA / protein-DNA complex / DNA repair / 5'-DNA end processing / Histidine Triad domain / HIT domain / Zinc-finger / 5'-DNA end recognition / HYDROLASE-DNA-RNA complex
Function / homology
Function and homology information


adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / single strand break repair / mismatched DNA binding / DNA ligation ...adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / single strand break repair / mismatched DNA binding / DNA ligation / phosphoprotein binding / regulation of protein stability / double-stranded RNA binding / single-stranded DNA binding / double-stranded DNA binding / damaged DNA binding / chromatin binding / chromatin / nucleolus / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / PNK, FHA domain / FHA domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain ...: / Aprataxin, C2HE/C2H2/C2HC zinc finger / C2HE / C2H2 / C2HC zinc-binding finger / Scavenger mRNA decapping enzyme C-term binding / PNK, FHA domain / FHA domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / SMAD/FHA domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BETA-MERCAPTOETHANOL / DNA / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchellenberg, M.J. / Tumbale, P.P. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: EMBO J. / Year: 2018
Title: Mechanism of APTX nicked DNA sensing and pleiotropic inactivation in neurodegenerative disease.
Authors: Tumbale, P. / Schellenberg, M.J. / Mueller, G.A. / Fairweather, E. / Watson, M. / Little, J.N. / Krahn, J. / Waddell, I. / London, R.E. / Williams, R.S.
History
DepositionMar 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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: Aprataxin
D: DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3')
B: Aprataxin
G: DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3')
E: DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')
H: DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,65012
Polymers59,6696
Non-polymers9826
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-57 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.913, 72.547, 147.164
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 / DNA/RNA hybrid / DNA chain , 3 types, 6 molecules ABDGEH

#1: Protein Aprataxin / Forkhead-associated domain histidine triad-like protein / FHA-HIT


Mass: 21259.756 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APTX, AXA1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z2E3, EC: 3.1.11.7, EC: 3.1.12.2
#2: DNA/RNA hybrid DNA/RNA (5'-R(P*G)-D(P*TP*TP*CP*TP*AP*TP*AP*TP*AP*TP*AP*GP*AP*AP*CP*GP*CP*TP*GP*TP*T)-3')


Mass: 6772.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized nucleic acid / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*AP*CP*AP*GP*C)-3')


Mass: 1802.232 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 410 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 100 mM MES, 16% w/v polyethylene glycol 3350 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 15, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25443 / % possible obs: 100 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.145 / Χ2: 1.142 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.4-2.494.50.57124960.863199.9
2.49-2.594.60.44325050.9181100
2.59-2.74.50.36924860.8861100
2.7-2.854.60.28425050.9761100
2.85-3.024.50.22425311.1211100
3.02-3.264.50.15425091.2811100
3.26-3.584.50.11525371.4471100
3.58-4.14.50.10225581.291100
4.1-5.174.40.09925911.3451100
5.17-504.20.0927251.296199.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDF

4ndf


Resolution: 2.4→43.673 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1292 5.09 %
Rwork0.1836 --
obs0.1856 25382 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→43.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 1146 56 404 4508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034356
X-RAY DIFFRACTIONf_angle_d0.5626122
X-RAY DIFFRACTIONf_dihedral_angle_d19.8252396
X-RAY DIFFRACTIONf_chiral_restr0.041672
X-RAY DIFFRACTIONf_plane_restr0.003566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.49640.25991500.22912620X-RAY DIFFRACTION100
2.4964-2.610.27031280.21752639X-RAY DIFFRACTION100
2.61-2.74760.28951320.22682644X-RAY DIFFRACTION100
2.7476-2.91970.25911330.2192654X-RAY DIFFRACTION100
2.9197-3.14510.27791490.19922638X-RAY DIFFRACTION100
3.1451-3.46150.22451550.18192678X-RAY DIFFRACTION100
3.4615-3.96210.19271600.16832657X-RAY DIFFRACTION100
3.9621-4.99070.18681390.14532713X-RAY DIFFRACTION100
4.9907-43.67990.18491460.17222847X-RAY DIFFRACTION100
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)
12.366-0.7187-0.13861.80661.24193.015-0.101-0.2272-0.00170.27810.0268-0.13760.3386-0.05460.05340.2525-0.0054-0.05650.16010.03790.260624.237913.66545.582
21.12590.5352-0.06111.8531.08831.4664-0.0003-0.05560.14410.10840.0299-0.3246-0.0868-0.1111-0.01660.23280.019-0.05020.1687-0.02470.246825.162823.926741.8384
31.4586-0.26970.02951.9114-0.22771.71570.0610.17540.23830.034-0.0712-0.38470.06740.12740.02790.1508-0.0022-0.00580.13370.02640.249226.015616.60534.478
42.1731.62260.86583.17780.68951.126-0.1440.17670.3986-0.38210.0451-0.0299-0.3394-0.04490.08940.27550.01350.01080.20720.03030.281918.531525.598228.9763
52.90311.2208-0.96413.0506-1.08473.4425-0.33410.13360.0432-0.49850.198-0.170.14560.56750.20290.2683-0.0549-0.04960.4030.02290.21911.330312.611218.7888
69.19351.9666-3.35557.0191-0.87998.55290.04320.3893-0.9851-0.92250.2574-0.19651.34910.3407-0.3050.42980.0635-0.04140.2786-0.04350.287112.34473.657621.5663
72.34991.60691.69680.90710.87521.07530.2092-0.3576-0.19180.06-0.1173-0.12670.2029-0.4117-0.1020.3505-0.0639-0.00930.3470.01590.2838-4.37515.397230.953
88.04820.33214.51113.5831-0.35254.4925-0.1170.1018-0.7742-0.67790.37270.86070.0162-1.7249-0.27020.629-0.0814-0.21490.87190.08840.5102-31.4723-17.252111.7364
91.8257-0.4450.15482.8127-1.94273.56620.24040.3702-0.3446-0.59450.16130.65470.7997-0.3712-0.37680.4103-0.0442-0.14890.3204-0.00980.3426-20.2581.2883-5.7555
102.1312-0.7013-0.48042.15170.17742.90050.03790.0914-0.4045-0.24320.09220.21240.43380.2993-0.10150.31030.0194-0.04230.2075-0.01110.2435-13.1835.9911-3.0808
113.53260.4869-0.21481.7155-0.39341.82690.26710.57650.1992-0.4798-0.2357-0.20460.23510.4319-0.06520.33030.0983-0.00870.32680.01160.1715-10.535213.5172-9.2839
121.5340.04070.54011.2371-0.54471.48930.18460.0134-0.15-0.1079-0.17530.01580.1789-0.00560.01350.27470.0082-0.02420.1829-0.00380.1854-11.45468.55123.8882
133.73370.3079-0.36042.3392-0.06743.43970.0190.3565-0.3919-0.2344-0.0454-0.06280.20930.07920.05120.20350.0115-0.03070.19970.00060.2145-3.9119.87428.0505
144.3126-2.1553-2.93365.39243.44734.64570.02910.6039-0.0156-0.8933-0.1557-0.4756-0.20660.98140.08440.34770.05860.09460.56210.04340.3121.24839.3279-9.6422
151.34350.235-1.84091.31310.11582.73540.09070.6876-0.4554-0.131-0.5923-0.22020.56831.56210.28380.34880.2068-0.00950.7541-0.02050.52674.49153.11932.4643
162.82380.9885-1.37224.2639-1.51514.3171-0.1061-0.05360.4863-0.2920.03330.2093-0.35910.0321-0.03790.2306-0.0365-0.04960.2838-0.00770.2654-1.089419.247613.5785
172.51371.4173-0.04596.7647-3.40426.1648-0.2587-0.11990.93980.50470.24890.2279-0.5739-0.5779-0.00920.24650.0162-0.00690.2223-0.06990.4275-10.097522.492915.4403
181.5828-0.01710.61430.45520.32250.98130.2026-0.3814-0.08630.0397-0.02120.01840.0603-0.1916-0.19050.3501-0.0965-0.05250.30750.05140.3088-10.52660.410922.0653
191.9549-0.25311.32652.98060.53239.41180.124-0.6950.5103-0.13780.3096-0.3487-1.514-0.6906-0.47140.4773-0.03530.03470.5069-0.08510.3714-1.931616.623540.2197
201.7859-0.3773-0.65163.382-0.93823.0299-0.477-0.7251-0.56580.61820.65210.1410.4013-1.1181-0.2230.63730.05460.07590.4633-0.00070.374610.49512.051959.5897
212.57170.00190.46610.8987-0.39920.2638-0.5836-0.26110.09060.8963-0.06360.0270.0379-0.41310.53911.0289-0.0670.16241.0664-0.2460.503812.350615.957773.4306
225.644-1.20970.77325.0599-0.76575.0744-0.4559-0.7344-0.45230.3251-0.09471.04490.8285-1.25340.47630.5881-0.16060.10160.568-0.08260.4188.377118.654565.6928
230.07990.162-0.08730.3362-0.20934.4890.12120.42860.3967-0.17840.72460.1416-0.4339-0.44750.92151.77440.5131-0.62791.37180.0530.3528-32.0326-11.399310.5912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 314 )
5X-RAY DIFFRACTION5chain 'A' and (resid 315 through 328 )
6X-RAY DIFFRACTION6chain 'A' and (resid 329 through 339 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 15 )
8X-RAY DIFFRACTION8chain 'D' and (resid 16 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 164 through 192 )
10X-RAY DIFFRACTION10chain 'B' and (resid 193 through 217 )
11X-RAY DIFFRACTION11chain 'B' and (resid 218 through 251 )
12X-RAY DIFFRACTION12chain 'B' and (resid 252 through 275 )
13X-RAY DIFFRACTION13chain 'B' and (resid 276 through 286 )
14X-RAY DIFFRACTION14chain 'B' and (resid 287 through 300 )
15X-RAY DIFFRACTION15chain 'B' and (resid 301 through 314 )
16X-RAY DIFFRACTION16chain 'B' and (resid 315 through 328 )
17X-RAY DIFFRACTION17chain 'B' and (resid 329 through 340 )
18X-RAY DIFFRACTION18chain 'G' and (resid 1 through 10 )
19X-RAY DIFFRACTION19chain 'G' and (resid 11 through 15 )
20X-RAY DIFFRACTION20chain 'G' and (resid 16 through 20 )
21X-RAY DIFFRACTION21chain 'G' and (resid 21 through 22 )
22X-RAY DIFFRACTION22chain 'E' and (resid 1 through 6 )
23X-RAY DIFFRACTION23chain 'H' and (resid 1 through 6 )

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