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- PDB-4ndg: Human Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanada... -

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Basic information

Entry
Database: PDB / ID: 4ndg
TitleHuman Aprataxin (Aptx) bound to RNA-DNA and Zn - adenosine vanadate transition state mimic 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-5'-vanadate / DNA / DNA/RNA hybrid / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 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)55,55710
Polymers54,7266
Non-polymers8314
Water45025
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)27,7785
Polymers27,3633
Non-polymers4162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area13060 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)27,7785
Polymers27,3633
Non-polymers4162
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-19 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.276, 114.580, 124.658
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 , 3 types, 29 molecules

#4: Chemical ChemComp-V5A / adenosine-5'-vanadate


Mass: 350.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O6V
#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.: 25 / 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: 53.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM sodium formate, 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: Feb 2, 2013
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: 2.541→50 Å / Num. all: 19773 / Num. obs: 19635 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 61.87 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.999 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.541-2.644.10.58219211.0611100
2.64-2.754.10.42519250.921100
2.75-2.874.10.28419510.974199.8
2.87-3.024.10.20219201.001199.9
3.02-3.214.10.11519571.005199.7
3.21-3.4640.08619541.002199.9
3.46-3.8140.08219611.005199.5
3.81-4.363.90.0719731.005199.2
4.36-5.493.80.06319981.015199
5.49-503.50.05520751196.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
PHENIX1.8.2_1309phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NDH

4ndh


Resolution: 2.541→39.063 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7468 / SU ML: 0.45 / σ(F): 1.37 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 1002 5.14 %RANDOM
Rwork0.2084 ---
obs0.211 19503 98.62 %-
all-19773 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.61 Å2 / Biso mean: 88.5488 Å2 / Biso min: 37.44 Å2
Refinement stepCycle: LAST / Resolution: 2.541→39.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 818 46 25 3810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154000
X-RAY DIFFRACTIONf_angle_d1.2235585
X-RAY DIFFRACTIONf_chiral_restr0.048606
X-RAY DIFFRACTIONf_plane_restr0.007553
X-RAY DIFFRACTIONf_dihedral_angle_d20.4841532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.541-2.67450.43161180.34422581269998
2.6745-2.84210.33371570.31425942751100
2.8421-3.06140.35411500.288226222772100
3.0614-3.36930.27261290.21842645277498
3.3693-3.85650.28371420.21552620276299
3.8565-4.85740.22941470.17842695284299
4.8574-39.06790.21411590.17172744290397
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)
15.0898-2.25051.05034.5717-2.58315.6213-0.2459-0.4711-0.68951.30960.23050.51230.3484-0.3035-0.00630.6834-0.0433-0.01020.41510.13060.4656-3.9355-28.6671-12.9645
29.0592.9007-7.19954.4908-4.92357.65370.3883-0.21.1441.70090.49470.0736-1.9365-0.3888-0.60741.79630.1475-0.10660.7610.11480.52236.4014-21.306-4.1782
36.31-0.36253.10596.2665-0.42578.2792-0.21480.291-0.23230.46680.2292-0.54650.22470.9253-0.07780.64470.0679-0.08310.5458-0.01310.4147.7793-26.0082-18.362
42.8566-2.79690.6198.8513-1.78385.6575-0.38271.0120.338-1.12380.0574-0.5889-0.72321.7550.33570.9651-0.28860.02270.90040.13830.58347.5859-17.5668-31.6528
54.3739-1.111-0.74849.0614-5.08854.8860.08090.48450.1762-0.88140.62290.4645-0.5498-0.5459-0.7571.0876-0.0675-0.19790.59620.04040.5017-10.0358-6.8902-29.0292
64.2702-2.4555-2.4451.62562.26396.71630.00080.24990.4638-0.65440.38270.11660.17250.471-0.27761.2119-0.1448-0.19460.53430.10040.5369-9.8548-6.1317-28.8061
70.3127-0.90450.10734.0631-1.11010.60061.65251.0003-0.9882-2.5907-0.45482.8870.8888-0.21551.12231.1650.3808-0.85240.7827-0.54821.25385.98498.9778-15.8088
86.63371.0395.10663.7013.10016.35980.04511.8181-0.0898-1.9379-0.59850.09290.64933.40691.22511.81550.7763-0.50842.45710.06710.869115.217416.3287-25.7886
94.3517-1.44611.61754.8381-1.98631.36950.54550.15550.5197-2.1342-0.87261.639-0.0486-0.05770.04380.74550.4743-0.49280.6794-0.29971.11278.389819.0411-12.1237
107.3209-3.84823.19929.4159-2.23812.9188-0.15610.08851.48180.6416-0.6004-0.7443-1.120.53040.53660.56790.1144-0.11910.5765-0.06210.968618.963721.6587-3.9872
115.987-1.39153.385.7865-2.36337.11250.9961-0.7945-0.58940.31540.12190.54691.00680.8213-0.91671.0820.386-0.07140.9128-0.13890.580825.37950.22531.4662
121.9657-1.4068-2.29784.31566.19679.5090.2661-0.8377-0.0560.05510.30090.06710.7190.5928-0.45581.06640.2027-0.03631.01950.00760.501126.25220.32840.9365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 206 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 217 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 300 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 340 )A0
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 10 )D0
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 10 )E0
7X-RAY DIFFRACTION7chain 'B' and (resid 164 through 206 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 207 through 217 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 218 through 275 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 276 through 340 )B0
11X-RAY DIFFRACTION11chain 'G' and (resid 1 through 10 )G0
12X-RAY DIFFRACTION12chain 'H' and (resid 1 through 10 )H0

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