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- PDB-4ndi: Human Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, ... -

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Basic information

Entry
Database: PDB / ID: 4ndi
TitleHuman Aprataxin (Aptx) AOA1 variant K197Q bound to RNA-DNA, AMP, and Zn - product complex
Components
  • 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
  • 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
  • Aprataxin
KeywordsDNA BINDING PROTEIN/RNA/DNA / protein-DNA complex / DNA repair / 5'-DNA end processing / Histidine Triad domain / HIT domain / Zinc finger / 5'-DNA end recognition / DNA BINDING PROTEIN-RNA-DNA 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 / phosphoglycolate phosphatase activity / single-strand break-containing DNA binding / 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 / phosphoglycolate phosphatase activity / single-strand break-containing DNA binding / 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 / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchellenberg, M.J. / Tumbale, P.S. / Williams, R.S.
CitationJournal: Nature / Year: 2013
Title: Aprataxin resolves adenylated RNA-DNA junctions to maintain genome integrity.
Authors: Tumbale, P. / Williams, J.S. / Schellenberg, M.J. / Kunkel, T.A. / Williams, R.S.
History
DepositionOct 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Aprataxin
B: Aprataxin
D: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
E: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
G: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
H: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,89816
Polymers54,7246
Non-polymers1,17510
Water12,574698
1
A: Aprataxin
D: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
E: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0079
Polymers27,3623
Non-polymers6456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-34 kcal/mol
Surface area12630 Å2
MethodPISA
2
B: Aprataxin
G: 5'-R(P*G)-D(P*TP*TP*AP*TP*GP*AP*TP*TP*C)-3'
H: 5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8927
Polymers27,3623
Non-polymers5304
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-21 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.468, 115.491, 116.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 21258.705 Da / Num. of mol.: 2 / Mutation: K197Q
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
#2: DNA/RNA hybrid 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
#3: DNA chain 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

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Non-polymers , 7 types, 708 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 200 mM potassium acetate, 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, temperature 277K

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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 16, 2012
RadiationMonochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 43956 / Num. obs: 43868 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4308 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NDH

4ndh


Resolution: 1.9→38.216 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8914 / SU ML: 0.17 / σ(F): 1.35 / Phase error: 17.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 2204 5.03 %RANDOM
Rwork0.1544 ---
obs0.1558 43811 99.84 %-
all-43956 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.45 Å2 / Biso mean: 21.7509 Å2 / Biso min: 3.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 818 65 698 4535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014195
X-RAY DIFFRACTIONf_angle_d1.2995888
X-RAY DIFFRACTIONf_chiral_restr0.078636
X-RAY DIFFRACTIONf_plane_restr0.005583
X-RAY DIFFRACTIONf_dihedral_angle_d20.121649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.94160.26481210.20392577269899
1.9416-1.98670.25631390.194225472686100
1.9867-2.03640.21771300.192325812711100
2.0364-2.09150.22681400.169925232663100
2.0915-2.1530.19991360.166225982734100
2.153-2.22250.18981220.163825742696100
2.2225-2.30190.21961450.159825472692100
2.3019-2.39410.1971370.167926112748100
2.3941-2.5030.23211400.163125702710100
2.503-2.63490.17861390.1625682707100
2.6349-2.80.1841340.161526082742100
2.8-3.01610.18751370.164926092746100
3.0161-3.31950.18121270.139926512778100
3.3195-3.79940.14261480.130226072755100
3.7994-4.78540.14851550.124926572812100
4.7854-38.22350.15661540.15712779293399
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)
12.50120.4048-0.73292.2995-3.1834.86790.01960.0277-0.08460.0837-0.1221-0.1013-0.01980.30470.08690.0807-0.0073-0.00820.09780.02320.112224.7997-19.0093-6.1183
22.79351.4494-0.01325.35320.04451.9549-0.0023-0.24890.10220.24290.0766-0.3974-0.16360.2399-0.00780.1521-0.0086-0.03660.1446-0.00230.103116.1604-17.34098.2571
31.16790.15690.35043.753-0.36191.0828-0.0110.00490.15250.127-0.0865-0.1012-0.17040.17730.04860.0775-0.0106-0.010.1232-0.010.067614.0968-7.39560.0359
40.85730.61120.46793.20710.14590.2618-0.01580.1301-0.1137-0.00170.0248-0.0494-0.00920.0229-0.03360.07770.01380.02890.11110.01480.075111.728-20.9691-3.5346
51.12721.64030.44996.49972.82843.13530.1088-0.19580.00630.4334-0.0147-0.01250.1379-0.1096-0.04560.07020.00870.00710.11920.0140.05593.7258-19.24673.3085
61.78050.52050.28810.6841-0.931.978-0.1816-0.32920.56140.25610.11880.0298-0.1635-0.3308-0.03310.09820.062-0.03850.1699-0.04110.13782.1401-6.1885-0.7036
71.4857-0.7609-0.22541.9887-0.88871.2237-0.04380.05010.11010.02920.05060.0058-0.0276-0.0457-0.01010.0678-0.0094-0.00790.08110.00460.077910.0056-7.4483-9.7483
81.61213.1052-0.98056.4557-2.28782.32060.07790.08280.10560.13790.05990.2331-0.0436-0.0712-0.12230.05750.00520.00060.10630.02530.0768-1.8067-20.4608-7.845
91.23872.2877-1.23494.4017-2.60353.1545-0.19640.1963-0.0438-0.78510.2043-0.16680.408-0.08060.06720.1612-0.0001-0.02280.16410.02880.10014.7953-17.2142-19.7441
103.4652-0.0363-1.27013.66341.11474.8144-0.04110.12850.3645-0.0436-0.09150.6224-0.314-0.47450.10540.11470.0224-0.03870.16090.03030.2391.01143.6249-15.893
116.12411.2448-1.82534.89570.29726.11390.334-0.42480.66230.299-0.22650.1822-0.52910.0113-0.00490.2102-0.00420.0130.10860.00150.21095.49659.1039-8.593
127.5865-0.6747-1.82291.46431.22443.65750.26490.14720.7044-0.25250.09290.3166-0.205-0.3872-0.35150.15520.0004-0.01570.170.05930.21910.2693-6.3962-28.6689
131.06770.44790.01513.0786-0.92072.24180.045-0.0610.07640.1117-0.1062-0.0549-0.14170.07790.06650.09540.0070.02260.15360.02730.07916.3681-10.1165-40.8324
143.0758-1.84490.46995.312-1.01482.99010.00010.19090.0785-0.2522-0.03530.0845-0.20180.11310.05630.1426-0.01480.00110.17430.04140.09776.1406-6.1285-51.5707
152.17820.58730.38223.9889-0.76352.8233-0.07830.1553-0.0644-0.20730.12480.05110.1277-0.0195-0.04340.10580.00180.00790.13610.00650.0733-0.4065-20.4985-44.6557
163.17391.1781-0.86985.5422-1.30751.74320.03860.3910.0113-0.38450.09260.55710.041-0.3029-0.15030.1452-0.0162-0.05550.24940.04230.2066-9.7449-10.9868-51.5428
174.58151.6677-1.36936.1714-0.92026.67290.01250.2425-0.7056-0.64240.02270.13590.73220.1540.01380.2862-0.0122-0.02240.12760.0120.2586-4.7913-34.5704-46.5716
181.922-1.45080.99543.7323-3.08063.79170.14130.11680.28450.0436-0.2907-0.0828-0.40850.41080.17420.1725-0.02510.01720.13980.02590.15423.19970.6564-20.9346
193.847-3.96750.59344.3728-0.52260.20140.12960.2962-0.1814-0.1099-0.19060.3779-0.10480.09360.06150.1718-0.0005-0.00950.15670.05690.196522.23840.5197-22.9789
202.41142.8250.60493.94060.49450.68240.3373-0.1642-0.08340.2885-0.49330.29710.1951-0.14480.14950.1981-0.04240.04070.198-0.03630.2194-12.2158-27.6344-26.6459
210.48680.78840.28389.17575.10293.71150.0642-0.1067-0.2582-0.3777-0.34880.3137-0.0953-0.37680.26540.1429-0.02250.00270.1670.00820.224-13.3126-27.1223-26.5197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 161 through 176 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 187 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 188 through 200 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 217 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 239 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 251 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 252 through 286 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 287 through 300 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 314 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 315 through 328 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 329 through 340 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 161 through 176 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 177 through 217 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 218 through 238 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 239 through 286 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 287 through 314 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 315 through 340 )B0
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 10 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 10 )E0
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 10 )G0
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 10 )H0

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