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

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Open data


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Basic information

Entry
Database: PDB / ID: 4ndf
TitleHuman Aprataxin (Aptx) 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 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 / BETA-MERCAPTOETHANOL / : / DNA / DNA/RNA hybrid / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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)55,76914
Polymers54,7266
Non-polymers1,0448
Water10,016556
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)27,9168
Polymers27,3633
Non-polymers5535
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-32 kcal/mol
Surface area12870 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)27,8546
Polymers27,3633
Non-polymers4913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-22 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.429, 116.211, 117.141
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: 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/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 , 6 types, 564 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 200 mM potassium sodium tartrate, 20% w/v PEG3350, 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: Dec 10, 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: 1.944→50 Å / Num. all: 41560 / Num. obs: 41518 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Χ2: 1.061 / Net I/σ(I): 16.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.944-2.023.90.58840960.974199.9
2.02-2.140.42340531.0591100
2.1-2.24.10.30640911.0911100
2.2-2.3140.22940841.14199.9
2.31-2.464.10.18241181.1811100
2.46-2.654.10.1341311.151100
2.65-2.914.10.09241521.13199.9
2.91-3.334.10.05641560.934199.9
3.33-4.23.90.04442131.054199.9
4.2-503.80.03344240.886199.6

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Processing

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

4ndh


Resolution: 1.944→32.409 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.865 / SU ML: 0.17 / σ(F): 1.36 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2082 5.02 %RANDOM
Rwork0.1712 ---
obs0.1729 41440 99.69 %-
all-41560 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.51 Å2 / Biso mean: 24.6341 Å2 / Biso min: 4.14 Å2
Refinement stepCycle: LAST / Resolution: 1.944→32.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 818 58 556 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094193
X-RAY DIFFRACTIONf_angle_d1.1545882
X-RAY DIFFRACTIONf_chiral_restr0.066633
X-RAY DIFFRACTIONf_plane_restr0.004579
X-RAY DIFFRACTIONf_dihedral_angle_d20.7041649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.944-1.98940.3171200.24482505262597
1.9894-2.03910.26971400.227926032743100
2.0391-2.09430.2831300.217225752705100
2.0943-2.15590.24931500.189625952745100
2.1559-2.22540.23171310.189525972728100
2.2254-2.3050.22771490.18125632712100
2.305-2.39720.22071360.186126172753100
2.3972-2.50630.2051350.187826182753100
2.5063-2.63840.23861300.18626122742100
2.6384-2.80360.24741400.18526202760100
2.8036-3.01990.22611450.184326162761100
3.0199-3.32350.19541350.155226642799100
3.3235-3.80380.16361550.146226292784100
3.8038-4.78990.16021250.136127222847100
4.7899-32.41350.17261610.168228222983100
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)
11.81220.1604-1.1042.0582-0.924.5177-0.1193-0.2321-0.2587-0.0941-0.1749-0.12960.08980.60.2510.1041-0.0181-0.01870.13140.04670.122224.8462-19.4886-6.7046
22.0381-0.7074-0.03173.6201-0.50153.224-0.1886-0.17660.20360.26380.2115-0.1185-0.27380.1079-0.00750.1482-0.003-0.00140.17730.0140.041615.8862-18.01088.3592
31.6009-0.0715-0.10113.6062-1.11151.7747-0.0396-0.2010.17380.2808-0.0627-0.239-0.3430.22340.0790.1039-0.0021-0.02380.0763-0.02240.048714.232-7.65640.0306
41.60911.22740.82352.9993-0.18171.13610.0031-0.0451-0.03720.09780.03710.03470.0452-0.0459-0.02960.0670.01370.01850.10360.02620.03877.1071-20.15880.4587
52.13750.72670.31741.6814-0.93573.3905-0.1799-0.31870.74190.05130.13380.136-0.3459-0.4784-0.11160.0760.0556-0.02040.1807-0.06050.22552.1727-6.2819-0.6701
61.9434-0.137-0.66361.5929-0.46741.3728-0.0350.09530.1595-00.00180.0016-0.0329-0.02750.02410.0568-0.0032-0.02390.06860.00720.036811.4985-8.5372-7.1087
71.72891.5374-0.12232.5305-0.41180.4842-0.1740.21420.3225-0.17110.28490.3265-0.0513-0.235-0.13380.11870.0037-0.02680.13390.04520.09632.3264-13.6854-10.9996
80.66280.9966-0.47332.3174-1.8421.9549-0.24710.3549-0.0214-1.28440.14560.02330.493-0.0403-0.05480.3233-0.0663-0.12790.23360.1965-0.41154.4645-16.6479-20.2346
93.42530.2835-0.2154.0688-0.08873.543-0.1458-0.25660.427-0.01430.04831.1798-0.4678-0.99540.01070.33010.0727-0.09790.34450.07950.42030.99113.541-15.77
102.01811.83431.03183.7382-2.45814.32630.1292-0.91551.37890.88560.08030.1522-1.1075-0.436-0.35110.45890.05110.03460.2354-0.01360.38325.44358.7663-8.6255
112.07851.5877-0.98822.8767-0.24153.23540.1074-0.08040.3210.0262-0.05740.2446-0.24820.1522-0.02090.11610.0089-0.00450.15570.05020.14266.6981-10.4252-35.7528
120.9370.27690.30693.0983-0.85462.74140.03010.17420.1613-0.08620.02090.1054-0.2042-0.1352-0.07780.14290.0060.01950.19930.07440.11053.7756-6.1466-48.4402
132.29320.46420.32784.3786-1.59412.7311-0.05380.37240.043-0.34570.16410.33110.1503-0.193-0.11130.1323-0.016-0.01650.17940.01660.1212-4.1638-16.8282-47.1593
145.75970.1976-0.20055.6338-0.85237.45890.06330.8615-1.0453-1.0827-0.1303-0.09491.23410.60960.06240.53880.0175-0.02260.2802-0.06130.3721-4.2059-34.6959-46.9683
150.8948-0.40490.66532.8133-2.22853.70460.13740.11140.2922-0.1676-0.3158-0.1243-0.52730.47330.31980.25390.00640.03910.13160.0670.247922.4321.0579-22.1385
164.1098-3.56740.49523.3424-0.6640.98120.28240.3382-0.2877-0.1741-0.32510.503-0.26450.12620.01420.24160.0129-0.03410.12680.04550.263921.3908-0.1963-23.7611
171.93421.47310.70072.7739-0.31421.84170.4855-0.2836-0.35150.7146-0.80180.65590.3834-0.11640.01280.3752-0.09520.13220.1405-0.12490.3558-12.1066-27.7657-27.0668
180.3159-0.68560.21926.0643.03652.70990.059-0.1047-0.5521-0.444-0.22440.5608-0.0435-0.34670.10260.3015-0.0470.02870.1140.01190.3476-13.135-27.3637-26.9704
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 239 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 240 through 251 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 275 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 300 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 314 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 315 through 328 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 329 through 340 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 200 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 201 through 239 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 240 through 314 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 315 through 340 )B0
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 10 )D0
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 10 )E0
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 10 )G0
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 10 )H0

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