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- PDB-6cvq: Human Aprataxin (Aptx) H201Q bound to RNA-DNA, AMP and Zn product... -

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Basic information

Entry
Database: PDB / ID: 6cvq
TitleHuman Aprataxin (Aptx) H201Q 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-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / polynucleotide 3'-phosphatase activity / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / 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 / single-strand break-containing DNA binding / phosphoglycolate phosphatase activity / 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: 1.65 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 ...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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aprataxin
B: 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')
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)55,43615
Polymers54,2476
Non-polymers1,1899
Water13,673759
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)27,8219
Polymers27,1243
Non-polymers6986
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)27,6146
Polymers27,1243
Non-polymers4913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.571, 116.049, 117.215
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: 21020.504 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain / Mutation: H201Q
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 / Details: Chemically synthesized nucleic acid / 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 , 6 types, 768 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.54 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 100 mM HEPES, 25% w/v polyethylene glycol 3350

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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: May 12, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 67271 / % possible obs: 99.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 12.69 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.034 / Rrim(I) all: 0.083 / Χ2: 0.874 / Net I/σ(I): 9.3 / Num. measured all: 393424
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.714.10.54262830.7910.2890.6170.79894.2
1.71-1.785.30.43466400.8910.2050.4810.84599.7
1.78-1.866.10.32266770.950.1410.3520.862100
1.86-1.966.20.22666820.9690.0980.2470.923100
1.96-2.086.20.15766970.9830.0680.1720.95100
2.08-2.246.20.11367430.990.0490.1240.945100
2.24-2.466.20.09267390.9920.040.1010.953100
2.46-2.826.20.06867860.9950.030.0740.838100
2.82-3.556.10.05868640.9960.0250.0630.901100
3.55-505.90.04471600.9970.020.0480.68499.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NDF

4ndf


Resolution: 1.65→32.409 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.33
RfactorNum. reflection% reflection
Rfree0.1677 5041 5.07 %
Rwork0.1178 --
obs0.1204 99412 77.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→32.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 818 69 759 4598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014187
X-RAY DIFFRACTIONf_angle_d0.9925842
X-RAY DIFFRACTIONf_dihedral_angle_d18.6972372
X-RAY DIFFRACTIONf_chiral_restr0.056634
X-RAY DIFFRACTIONf_plane_restr0.006579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6499-1.66860.2332790.17271443X-RAY DIFFRACTION36
1.6686-1.68830.2465970.17051635X-RAY DIFFRACTION40
1.6883-1.70890.2558770.16251796X-RAY DIFFRACTION44
1.7089-1.73050.2341100.15441937X-RAY DIFFRACTION48
1.7305-1.75330.18461150.15852087X-RAY DIFFRACTION51
1.7533-1.77730.18961250.15192058X-RAY DIFFRACTION51
1.7773-1.80270.21281050.14912134X-RAY DIFFRACTION52
1.8027-1.82960.1921010.14352161X-RAY DIFFRACTION53
1.8296-1.85820.21511140.13922149X-RAY DIFFRACTION53
1.8582-1.88860.21391360.13382213X-RAY DIFFRACTION55
1.8886-1.92120.16471350.12442362X-RAY DIFFRACTION58
1.9212-1.95610.16181020.11912530X-RAY DIFFRACTION62
1.9561-1.99370.15071520.10772727X-RAY DIFFRACTION67
1.9937-2.03440.17291540.10413175X-RAY DIFFRACTION77
2.0344-2.07870.15671640.10453393X-RAY DIFFRACTION84
2.0787-2.1270.17731740.10573821X-RAY DIFFRACTION92
2.127-2.18020.18242230.1073926X-RAY DIFFRACTION98
2.1802-2.23910.14212040.10824099X-RAY DIFFRACTION100
2.2391-2.3050.17312150.10164017X-RAY DIFFRACTION100
2.305-2.37940.17742100.10834154X-RAY DIFFRACTION100
2.3794-2.46440.17722040.114045X-RAY DIFFRACTION100
2.4644-2.5630.18762220.11454071X-RAY DIFFRACTION100
2.563-2.67960.16212370.11424043X-RAY DIFFRACTION100
2.6796-2.82080.20352400.11894038X-RAY DIFFRACTION100
2.8208-2.99740.16112340.12574051X-RAY DIFFRACTION100
2.9974-3.22860.16172130.11694078X-RAY DIFFRACTION100
3.2286-3.55320.13282010.11034084X-RAY DIFFRACTION100
3.5532-4.06650.16412390.10744064X-RAY DIFFRACTION100
4.0665-5.12010.13222280.10784059X-RAY DIFFRACTION100
5.1201-32.41530.17932310.15154021X-RAY DIFFRACTION100

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