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- PDB-4ndh: Human Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex -

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Basic information

Entry
Database: PDB / ID: 4ndh
TitleHuman Aprataxin (Aptx) bound to DNA, AMP, and Zn - product complex
Components
  • 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
  • Aprataxin
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / DNA repair / 5'-DNA end processing / Histidine Triad domain / HIT domain / Zinc finger / 5'-DNA end recognition / DNA BINDING PROTEIN-DNA 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 / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 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_label_asym_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_label_asym_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'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
E: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
G: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
H: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,52110
Polymers54,6966
Non-polymers8254
Water9,026501
1
A: Aprataxin
D: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
E: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7605
Polymers27,3483
Non-polymers4132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-25 kcal/mol
Surface area13090 Å2
MethodPISA
2
B: Aprataxin
G: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
H: 5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7605
Polymers27,3483
Non-polymers4132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-20 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.397, 117.082, 118.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21259.756 Da / Num. of mol.: 2
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 chain
5'-D(P*GP*TP*TP*CP*TP*AP*GP*AP*AP*C)-3'


Mass: 3044.017 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 52.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 100 mM Tris, 20% w/v PEG10000, pH 8.5, 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: Nov 20, 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: 1.848→50 Å / Num. all: 49053 / Num. obs: 48759 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 25.07 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.003 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.848-1.923.30.43647471.003198.5
1.92-1.993.90.32648051.004199.9
1.99-2.083.90.23148381.013199.9
2.08-2.193.90.16348321.01199.9
2.19-2.333.90.12448351.01199.8
2.33-2.513.90.10548750.99199.7
2.51-2.763.90.08248660.998199.5
2.76-3.163.90.05548881.003199.3
3.16-3.993.70.04949420.998199.2
3.99-503.60.03451311.002198.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SZQ

3szq


Resolution: 1.848→32.687 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8748 / SU ML: 0.15 / σ(F): 1.35 / Phase error: 19.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 2457 5.05 %RANDOM
Rwork0.1625 ---
obs0.1642 48675 99.37 %-
all-49053 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.29 Å2 / Biso mean: 29.3702 Å2 / Biso min: 5.82 Å2
Refinement stepCycle: LAST / Resolution: 1.848→32.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 824 48 501 4317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054247
X-RAY DIFFRACTIONf_angle_d1.0995977
X-RAY DIFFRACTIONf_chiral_restr0.066646
X-RAY DIFFRACTIONf_plane_restr0.004591
X-RAY DIFFRACTIONf_dihedral_angle_d19.8891682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.848-1.8840.25971200.21942475259597
1.884-1.92240.23811310.206625902721100
1.9224-1.96420.24441330.199424842617100
1.9642-2.00990.23651450.184325422687100
2.0099-2.06020.21951520.178225262678100
2.0602-2.11590.21921410.170125402681100
2.1159-2.17810.19441200.168525562676100
2.1781-2.24840.22471380.168525902728100
2.2484-2.32870.21341300.168825102640100
2.3287-2.4220.26051240.174725782702100
2.422-2.53210.21421530.173225682721100
2.5321-2.66560.2221420.178925482690100
2.6656-2.83250.22711380.17792547268599
2.8325-3.05110.21621390.18032579271899
3.0511-3.35780.1651170.15192623274099
3.3578-3.84310.17991320.13842584271699
3.8431-4.83930.15321610.12772617277899
4.8393-32.69190.17711410.16732761290298
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)
11.2187-1.41280.07772.68080.62541.6688-0.0003-0.06030.24280.24840.1332-0.5374-0.08170.1108-0.1010.128-0.0032-0.01230.1552-0.0520.177214.419422.8319-9.6916
21.25950.4688-0.14441.72030.29512.3958-0.00870.04720.1044-0.0593-0.009-0.0835-0.2050.12840.01410.06990.0118-0.00460.0893-0.00360.14233.419430.5411-12.9497
32.18751.8731-2.28353.9248-4.19276.58880.10520.19910.2360.1392-0.12180.0531-0.57950.1466-0.2340.14350.03340.00720.1067-0.01670.1803-6.779233.2567-11.1627
42.5322-1.6211.12632.9647-2.15174.83940.10930.34610.1304-0.0670.07860.5695-0.14-0.31310.0860.0911-0.0074-0.03910.13550.03280.1743-7.606226.9094-20.9513
51.8946-0.60140.34591.56870.88042.7989-0.05580.12230.0102-0.15910.041-0.0076-0.10850.00310.01030.1027-0.02450.00170.0912-0.01320.14921.259622.4192-20.5166
63.8183-1.311-4.56950.79812.44647.1428-0.07570.1677-0.1427-0.0691-0.16420.23540.0414-0.3280.27080.1357-0.0024-0.0090.109-0.01250.1713-7.855918.1005-15.5276
70.8263-0.6613-1.6771.68752.12474.012-0.30550.0032-0.14770.63880.07230.27851.5829-0.06270.04530.3814-0.04790.03030.188-0.04680.3214-5.50469.1295-13.1882
84.0566-2.85961.83083.9439-0.88774.32930.01010.1524-0.0974-0.3213-0.06390.72110.0666-0.53620.07370.3066-0.0732-0.04810.3322-0.07460.3118-8.831313.312-32.8104
95.3605-5.0759-0.93747.96430.75074.28890.24540.81170.6414-0.7842-0.20690.1599-0.9064-0.12230.00140.3963-0.0357-0.00540.3095-0.00320.2802-3.881720.593-37.7506
105.02192.234-1.56045.8769-0.39585.1357-0.0872-0.43440.24220.2127-0.10360.18660.09940.29480.20490.25780.01240.04690.21030.03040.22399.596958.8978-35.4898
112.21980.299-0.78263.1207-0.93913.31370.0498-0.19590.11750.17770.11350.1988-0.1106-0.2181-0.08550.1027-0.01660.01060.12180.0260.16033.999246.9258-39.088
126.6706-1.24424.04773.0315-1.86134.53340.0466-0.1898-0.3610.10730.05910.16510.3051-0.1441-0.14410.1687-0.02430.00990.15980.06080.22753.83836.328-35.1315
134.89541.26522.20222.89771.76046.7790.1411-0.1317-0.3748-0.0174-0.20280.26140.854-0.49080.1580.2146-0.0432-0.00550.1274-0.00510.26253.39636.6327-50.2274
142.58230.3204-0.93092.526-1.29826.2823-0.0562-0.04620.0086-0.112-0.0564-0.13180.01380.2920.07730.1530.00510.00230.12530.00890.168913.722745.3902-48.9398
152.6986-1.41362.47816.8241-4.16925.3984-0.1863-0.1716-0.7606-0.33350.0189-0.15390.9216-0.026-0.16010.26090.05840.02870.21680.0860.327214.956531.8171-37.1942
160.1119-0.06490.27221.9907-1.76551.9539-0.2871-0.1283-0.6357-0.34-0.4912-0.83210.40881.21180.70340.20.08230.05030.46650.11260.378125.437940.1349-42.0002
175.1230.9489-0.14516.0873-0.14845.6341-0.19870.6251-0.7307-0.6860.10610.07210.7580.12170.08040.4760.00120.06260.331-0.06510.265415.138140.4671-63.252
181.36020.00220.35512.92032.34883.45140.10890.2875-0.0167-0.28750.3037-0.32540.24180.3416-0.25510.20570.013-0.03830.2561-0.05850.138712.931110.0084-29.9759
191.7245-0.1121.73540.48270.16631.8040.00340.113-0.3687-0.27040.1163-0.07460.1473-0.23090.01430.2501-0.0438-0.01520.3479-0.08470.120312.63227.1891-31.1701
202.3384-0.1417-1.07710.6468-0.23442.59160.27450.42880.214-0.42920.2451-0.31790.00450.3934-0.0440.2887-0.03120.10850.299-0.05330.219422.995760.4074-57.2405
21-0.0537-0.4771-0.36492.26022.36373.90540.00960.2881-0.0382-0.22560.3886-0.40320.19510.7104-0.08440.3237-0.04590.04510.4191-0.04060.18823.732460.5291-56.9714
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 217 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 242 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 251 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 275 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 300 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 301 through 314 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 315 through 328 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 329 through 340 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 176 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 177 through 217 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 218 through 238 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 239 through 251 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 286 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 287 through 300 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 301 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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