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- PDB-6cvt: Human Aprataxin (Aptx) V263G bound to RNA-DNA, AMP and Zn product... -

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Basic information

Entry
Database: PDB / ID: 6cvt
TitleHuman Aprataxin (Aptx) V263G 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 / 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 / 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: 2.941 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
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')
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)55,46710
Polymers54,6416
Non-polymers8254
Water19811
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)27,7335
Polymers27,3213
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-23 kcal/mol
Surface area12700 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)27,7335
Polymers27,3213
Non-polymers4132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-23 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.727, 113.131, 124.500
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: 21217.676 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain / Mutation: V263G
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, 15 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 100 mM MES, 20% w/v polyethylene glycol 3350 / PH range: 6.5

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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: Jul 11, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→50 Å / Num. obs: 12827 / % possible obs: 99.4 % / Redundancy: 4 % / Biso Wilson estimate: 60.353 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Χ2: 0.765 / Net I/σ(I): 7.6 / Num. measured all: 50676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.94-3.053.90.40612060.8780.230.4690.66396.9
3.05-3.173.90.21312680.9830.1180.2450.73699.2
3.17-3.314.10.12912420.9940.0680.1470.833100
3.31-3.494.10.12312670.9930.0650.140.885100
3.49-3.740.09812890.9940.0530.1120.886100
3.7-3.994.10.08712540.9920.0470.0990.784100
3.99-4.3940.06212870.9940.0340.0720.729100
4.39-5.0340.05113020.9960.0280.0580.719100
5.03-6.333.90.04513170.9930.0260.0520.656100
6.33-503.60.03313950.9970.020.0390.7498

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDH

4ndh


Resolution: 2.941→38.961 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 556 4.78 %
Rwork0.2462 --
obs0.2482 11635 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.941→38.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 818 48 11 3781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113978
X-RAY DIFFRACTIONf_angle_d1.4355561
X-RAY DIFFRACTIONf_dihedral_angle_d20.6341542
X-RAY DIFFRACTIONf_chiral_restr0.041603
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9411-3.23690.38151220.30722086X-RAY DIFFRACTION71
3.2369-3.7050.33491160.28062791X-RAY DIFFRACTION91
3.705-4.66670.2881550.23933026X-RAY DIFFRACTION100
4.6667-38.96470.24761630.22193176X-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)
10.0293-0.02690.00480.02060.00730.0906-0.0864-0.0162-0.04330.2271-0.1845-0.0349-0.3785-0.1214-0.00620.28140.02780.02940.22360.07660.3647-4.1527-28.5829-12.3152
20.0031-0.00210.0031-0.0009-0.00180.0018-0.0211-0.02440.08760.00550.0010.0124-0.0457-0.0393-0.00010.96290.1517-0.28940.5785-0.13920.39326.3447-21.1764-4.2353
30.1223-0.09670.04240.14640.00690.0526-0.1811-0.0184-0.09410.25460.05830.02470.03690.2288-0.13680.13580.1533-0.30720.22360.06760.13627.5771-26.053-18.3725
40.0502-0.0261-0.03380.03970.00350.0301-0.1210.1306-0.154-0.0655-0.0725-0.0934-0.04580.122-0.00020.4849-0.134-0.12320.3697-0.01610.38677.6609-17.7647-31.38
50.0208-0.009-0.01750.00150.00110.010.2813-0.2826-0.21190.01940.2607-0.00460.19080.10010.00030.31340.06-0.10330.41830.1150.4941-10.1574-6.7715-28.8564
6-0.0041-0.0084-0.00920.0229-0.00630.00580.0961-0.11710.1633-0.12580.21450.0818-0.02350.12160.00060.6122-0.1478-0.0980.38110.00060.3871-9.8503-6.2434-28.663
70.0453-0.04430.0110.0378-0.01240.01040.00390.0685-0.0099-0.0705-0.11480.2168-0.0731-0.0722-0.06480.22150.3615-0.57780.2291-0.12710.80566.77228.9755-16.0935
80.00040.0007-0.0020.00010.00250.0033-0.04280.00940.0652-0.0419-0.0997-0.0941-0.02350.06410.00011.50720.21390.02621.45830.00711.110616.593318.3587-27.0566
90.0042-0.01520.00990.0463-0.02670.01610.00260.0296-0.0033-0.1306-0.1490.1195-0.08030.13040.01730.48370.5578-0.58590.4163-0.1340.79158.131619.8618-13.704
100.23830.1670.06640.16130.11590.2696-0.35710.14380.46730.266-0.0031-0.4113-0.33030.2451-0.01950.420.2887-0.25660.5340.08210.701818.822720.1217-3.3442
110.06090.05040.01680.1515-0.12630.1540.25020.01820.0774-0.15780.09960.2284-0.00260.07540.04870.66390.2908-0.08880.4701-0.01520.436125.5645-0.33391.7367
12-0.00510.0020.00250.0082-0.01170.0180.0366-0.2930.2024-0.19480.1151-0.09020.05790.03310.00040.81890.2013-0.0740.747-0.01330.558326.3649-0.0231.2138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 164:206 )A164 - 206
2X-RAY DIFFRACTION2( CHAIN A AND RESID 207:217 )A207 - 217
3X-RAY DIFFRACTION3( CHAIN A AND RESID 218:300 )A218 - 300
4X-RAY DIFFRACTION4( CHAIN A AND RESID 301:340 )A301 - 340
5X-RAY DIFFRACTION5( CHAIN D AND RESID 1:10 )D1 - 10
6X-RAY DIFFRACTION6( CHAIN E AND RESID 1:10 )E1 - 10
7X-RAY DIFFRACTION7( CHAIN B AND RESID 164:206 )B164 - 206
8X-RAY DIFFRACTION8( CHAIN B AND RESID 207:220 )B207 - 220
9X-RAY DIFFRACTION9( CHAIN B AND RESID 221:265 )B221 - 265
10X-RAY DIFFRACTION10( CHAIN B AND ( RESID 266:339 OR RESID 401:401 ) )B266 - 339
11X-RAY DIFFRACTION10( CHAIN B AND ( RESID 266:339 OR RESID 401:401 ) )B401
12X-RAY DIFFRACTION11( CHAIN G AND RESID 1:10 )G1 - 10
13X-RAY DIFFRACTION12( CHAIN H AND RESID 1:10 )H1 - 10

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