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- PDB-6cvr: Human Aprataxin (Aptx) S242N bound to RNA-DNA, AMP and Zn product... -

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Basic information

Entry
Database: PDB / ID: 6cvr
TitleHuman Aprataxin (Aptx) S242N bound to RNA-DNA, AMP and Zn product complex
Components
  • Aprataxin
  • DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
  • DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-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 / HYDROLASE-DNA-RNA complex
Function / homology
Function and homology information


adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / DNA-3'-diphospho-5'-guanosine diphosphatase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / mismatched DNA binding / single strand break repair / phosphoprotein binding ...adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / DNA-3'-diphospho-5'-guanosine diphosphatase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / mismatched DNA binding / single strand break repair / phosphoprotein binding / regulation of protein stability / single-stranded DNA binding / double-stranded RNA binding / double-stranded DNA binding / damaged DNA binding / chromatin binding / chromatin / nucleolus / zinc ion binding / nucleoplasm / nucleus / 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 / DNA / DNA/RNA hybrid / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSchellenberg, M.J. / Tumbale, P.S. / 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 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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
B: Aprataxin
D: DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3')
E: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
G: DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,60510
Polymers54,7806
Non-polymers8254
Water10,611589
1
A: Aprataxin
D: DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3')
E: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8025
Polymers27,3903
Non-polymers4132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-21 kcal/mol
Surface area13140 Å2
MethodPISA
2
B: Aprataxin
G: DNA/RNA (5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8025
Polymers27,3903
Non-polymers4132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-21 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.616, 116.056, 117.563
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: 21286.779 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain / Mutation: S242N
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*AP*TP*GP*AP*TP*TP*C)-3')


Mass: 3066.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3')


Mass: 3037.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 593 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 200 mM ammonium formate, 20% w/v polyethylene glycol 3350
PH range: 7.5

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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: Dec 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 44982 / % possible obs: 97.3 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.582 Å2 / Net I/σ(I): 17
Reflection shellResolution: 1.88→1.95 Å

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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: 1.88→38.39 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 2167 5.07 %
Rwork0.1661 --
obs0.1673 42724 92.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2948 818 48 589 4403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094023
X-RAY DIFFRACTIONf_angle_d1.0015608
X-RAY DIFFRACTIONf_dihedral_angle_d18.3272252
X-RAY DIFFRACTIONf_chiral_restr0.056610
X-RAY DIFFRACTIONf_plane_restr0.006558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8802-1.92390.2709570.21981142X-RAY DIFFRACTION40
1.9239-1.9720.24521060.21471955X-RAY DIFFRACTION68
1.972-2.02530.23191370.20392628X-RAY DIFFRACTION90
2.0253-2.08490.21721500.19312743X-RAY DIFFRACTION96
2.0849-2.15220.17671380.18352842X-RAY DIFFRACTION98
2.1522-2.22910.19231540.17372858X-RAY DIFFRACTION99
2.2291-2.31840.17981460.16792858X-RAY DIFFRACTION99
2.3184-2.42390.20221750.18342854X-RAY DIFFRACTION99
2.4239-2.55160.19011610.17162903X-RAY DIFFRACTION99
2.5516-2.71150.21931660.1812901X-RAY DIFFRACTION99
2.7115-2.92070.19921670.17522886X-RAY DIFFRACTION99
2.9207-3.21450.191540.16242908X-RAY DIFFRACTION100
3.2145-3.67940.18051620.14562964X-RAY DIFFRACTION100
3.6794-4.63440.16691440.14112975X-RAY DIFFRACTION100
4.6344-38.39750.17261500.16313140X-RAY DIFFRACTION99
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)
10.9190.0011-0.21590.863-0.97062.77860.0323-0.092-0.1343-0.0682-0.1141-0.14140.25840.57140.03740.098-0.0055-0.01050.16150.05010.119924.8252-19.2002-6.4657
22.1605-0.3396-0.08753.60760.2782.6603-0.091-0.25470.18130.11240.0905-0.3115-0.16730.2448-0.10130.1205-0.00860.00380.2009-0.02490.082116.3946-17.48978.1959
30.82980.27460.24021.558-0.25071.0368-0.01920.00060.04420.0384-0.0296-0.09980.00420.03190.04030.04740.00780.01410.11760.00950.083912.9857-15.006-1.942
41.15611.12980.59635.7772.66312.71480.0635-0.21980.06780.30130.02760.00420.1337-0.0138-0.06220.07650.00310.02340.14190.01080.11453.8565-19.32283.3837
53.3924-0.1293-0.30043.106-0.30422.6102-0.1147-0.3760.58270.26250.18210.324-0.3562-0.07520.17460.05460.0147-0.05650.154-0.02770.22382.5781-6.7107-0.09
60.79380.0231-0.16310.87010.05031.117-0.01160.05650.1631-0.0408-0.00040.0344-0.0875-0.02450.02510.0704-0.0056-0.0230.11410.02560.133211.631-8.4838-7.1105
71.08111.7232-0.39323.7119-0.9190.4178-0.18120.18210.3086-0.09280.23920.2337-0.0776-0.15930.00790.1044-0.0097-0.04470.15650.06340.15542.564-13.5778-11.1087
8-0.00780.0171-0.03460.4809-0.83251.4433-0.24850.13740.1823-0.75380.18160.28640.2714-0.01290.07270.3244-0.0864-0.07620.25490.07660.16894.2796-16.5714-20.2462
93.41753.01910.7393.44591.23230.8391-0.0353-0.24260.5972-0.18230.00271.0776-0.4527-0.4625-0.8160.38650.0336-0.13610.32490.1920.58121.11653.6919-15.6976
103.6464-0.1619-2.2861.2213-0.20465.0444-0.0271-0.11270.65320.39920.1565-0.0639-0.7119-0.3182-0.04380.39820.06960.04390.21390.05270.35825.69788.9034-8.612
111.16161.0684-0.44352.0521-0.15372.40440.1426-0.04860.07210.1515-0.19820.0266-0.15160.22390.01790.1313-0.00310.00220.21740.06070.18116.8178-10.5431-36.1614
121.55350.15490.28392.313-0.45281.79350.0330.1480.251-0.07140.02270.089-0.2387-0.1386-0.06150.16540.04910.06330.26620.09610.1833.7659-6.4552-48.2476
132.08910.4573-0.31393.0371-1.31681.9854-0.07770.38850.1258-0.38390.16430.24230.27-0.1018-0.09520.2151-0.0267-0.02340.25620.02320.1601-4.1176-16.9445-47.4313
141.55570.1451-0.96221.91290.27632.8451-0.14880.5269-0.7194-0.88750.10970.00561.0839-0.0371-0.0080.7857-0.03060.06480.3375-0.06360.4803-5.0091-34.499-47.0352
150.3824-0.11910.40211.1292-1.10161.85720.03660.07580.2497-0.1207-0.3125-0.0559-0.28020.33470.010.2347-00.02010.16780.10240.303422.57250.8696-22.3813
162.4166-1.55670.59671.0417-0.49030.37710.15520.3489-0.187-0.2714-0.18130.5116-0.2080.147-0.21880.2540.0128-0.03570.12480.07290.335922.22050.3859-23.4258
171.37780.5050.45851.686-1.11291.33690.2862-0.0412-0.30310.345-0.58430.38020.4498-0.0171-0.34070.3227-0.11240.10620.1359-0.13360.2732-12.0942-27.8645-26.9255
180.06540.01070.07721.87411.56751.37340.0995-0.1329-0.3749-0.3828-0.08650.13160.0914-0.23790.13010.3243-0.0561-0.02410.1262-0.00440.3124-13.2514-27.4666-26.8756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 176 )
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 187 )
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 239 )
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 251 )
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 275 )
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 300 )
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 314 )
9X-RAY DIFFRACTION9chain 'A' and (resid 315 through 328 )
10X-RAY DIFFRACTION10chain 'A' and (resid 329 through 340 )
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 200 )
12X-RAY DIFFRACTION12chain 'B' and (resid 201 through 238 )
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 314 )
14X-RAY DIFFRACTION14chain 'B' and (resid 315 through 340 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 10 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 10 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 10 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 10 )

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