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- PDB-6cvp: Human Aprataxin (Aptx) R199H bound to RNA-DNA, AMP and Zn product... -

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Basic information

Entry
Database: PDB / ID: 6cvp
TitleHuman Aprataxin (Aptx) R199H 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 / DNA / DNA/RNA hybrid / Aprataxin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsSchellenberg, M.J. / Williams, R.S. / Tumbale, P.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 1.2Feb 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)55,53611
Polymers54,6886
Non-polymers8485
Water9,170509
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)27,7565
Polymers27,3443
Non-polymers4132
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)27,7796
Polymers27,3443
Non-polymers4363
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.507, 121.105, 122.314
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: 21240.709 Da / Num. of mol.: 2 / Fragment: Aprataxin catalytic Domain / Mutation: R199H
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 , 4 types, 514 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: 100 mM MES, 20% 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 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39638 / % possible obs: 97.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.772 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.778 / Net I/σ(I): 10.5 / Num. measured all: 131390
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2-2.0720.47533600.692183.9
2.07-2.152.70.40237390.794193.6
2.15-2.253.30.29739150.777198.1
2.25-2.373.50.23740260.769199.9
2.37-2.523.60.18540480.7571100
2.52-2.713.60.12540460.7651100
2.71-2.993.60.08240710.768199.9
2.99-3.423.60.04140710.865199.9
3.42-4.313.60.02741500.78199.5
4.31-503.50.02142120.766196.6

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Processing

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

4ndf


Resolution: 1.999→27.624 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2138 2847 5.04 %
Rwork0.1644 --
obs0.1668 56543 73.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→27.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 818 49 509 4296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114011
X-RAY DIFFRACTIONf_angle_d0.9835585
X-RAY DIFFRACTIONf_dihedral_angle_d17.7872233
X-RAY DIFFRACTIONf_chiral_restr0.057606
X-RAY DIFFRACTIONf_plane_restr0.007552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9988-2.03330.2807410.242770X-RAY DIFFRACTION21
2.0333-2.07020.2976610.2437996X-RAY DIFFRACTION27
2.0702-2.110.2437690.22261330X-RAY DIFFRACTION37
2.11-2.15310.2392900.21411682X-RAY DIFFRACTION46
2.1531-2.19990.30341070.21151912X-RAY DIFFRACTION52
2.1999-2.2510.23081130.19412098X-RAY DIFFRACTION59
2.251-2.30730.23881400.1952294X-RAY DIFFRACTION63
2.3073-2.36970.25841460.18642479X-RAY DIFFRACTION69
2.3697-2.43930.25621470.19342723X-RAY DIFFRACTION75
2.4393-2.5180.25721550.19333001X-RAY DIFFRACTION82
2.518-2.6080.22681380.18523239X-RAY DIFFRACTION88
2.608-2.71230.25322190.19643307X-RAY DIFFRACTION92
2.7123-2.83560.25191720.20413500X-RAY DIFFRACTION95
2.8356-2.98490.25341630.20423452X-RAY DIFFRACTION95
2.9849-3.17170.2141850.17643448X-RAY DIFFRACTION95
3.1717-3.41620.21111750.15773487X-RAY DIFFRACTION96
3.4162-3.75920.20861810.13793514X-RAY DIFFRACTION96
3.7592-4.30140.17061850.13363522X-RAY DIFFRACTION96
4.3014-5.41270.16932060.12193441X-RAY DIFFRACTION96
5.4127-27.62680.18131540.15043501X-RAY DIFFRACTION95
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)
11.53320.21520.30920.0612-0.17031.70990.03750.42880.3247-0.3029-0.0549-0.0305-0.44960.22470.16230.6123-0.02250.03350.18960.05930.235319.027821.48620.2627
20.06160.01340.18470.9795-0.03090.5784-0.1758-0.04960.14330.03310.0124-0.1196-0.7545-0.2515-0.18510.42440.2119-0.00610.008-0.02890.169212.617817.04324.2868
30.2259-0.06650.15650.2288-0.13030.2098-0.11730.00830.1526-0.13170.0240.0728-0.1329-0.143-0.15090.62350.2966-0.21450.29760.0150.14034.320319.0178-3.3932
41.617-0.06520.21991.4362-0.26590.9047-0.05870.0765-0.1308-0.04640.01490.0816-0.2215-0.16270.03670.20880.0722-0.01970.16540.00670.180611.1318.44235.0225
51.3756-1.15740.32661.5444-0.26571.282-0.0748-0.23460.14110.05650.00210.3352-0.741-0.9057-0.10810.13510.3622-0.02230.37570.03680.25712.382112.565713.0629
61.19550.291-0.27890.82180.35792.8775-0.0509-0.1445-0.24430.11430.12170.3280.5692-0.276-0.05250.21380.0158-0.00760.27380.06910.31728.8678-7.134310.6264
70.49360.13840.22052.2233-1.34351.03170.2506-0.2058-0.20060.215-0.2928-0.20.20540.12390.040.2678-0.0089-0.0880.25760.06290.346824.20542.547323.7489
80.92041.7008-0.13973.1989-0.20630.23430.2882-0.3018-0.02050.4439-0.31880.48080.22110.118-0.06390.2821-0.0375-0.03370.19140.02970.364523.77942.877124.6809
92.30690.37621.35931.79430.31212.74470.10120.1879-0.2067-0.2739-0.03-0.04970.14830.4142-0.01540.20250.01390.0030.3207-0.04520.18371.437514.692833.168
102.33840.5669-0.59471.8534-0.31271.17580.02250.2539-0.0279-0.09590.0519-0.3153-0.0540.4650.12380.1182-0.05150.01410.3624-0.02180.306712.91516.25742.507
111.0837-0.03080.12751.1780.12691.56670.02090.1064-0.1293-0.13010.0152-0.0388-0.18270.1864-0.03540.1446-0.0491-0.02610.1593-0.00980.19741.667517.397744.5072
122.04751.53630.10954.91020.08111.58980.0232-0.0517-0.11560.10360.1356-0.1301-0.01750.2474-0.12170.12550.0093-0.00190.22540.00710.17037.194613.345153.6384
131.096-0.60770.11931.2711-0.11951.4325-0.0139-0.08270.09780.06370.0658-0.0318-0.37070.0367-0.04840.164-0.00390.00770.1476-0.02390.1605-3.852124.741748.3883
141.775-0.97640.47081.8927-0.4030.6461-0.035-0.4364-0.47610.24680.1750.5552-0.0061-0.4402-0.02450.1890.03060.0850.28830.05250.3579-9.683112.230754.1882
151.1-0.810.63071.221-0.90222.5765-0.0929-0.25420.20490.11570.09020.0118-0.16770.18080.07570.27910.0641-0.00450.3247-0.040.3215-14.579333.714754.8703
160.56780.82811.72442.74830.99517.7850.192-0.25140.28290.1465-0.1474-0.4745-0.43020.68120.07550.4764-0.1287-0.0020.3684-0.03230.3241-7.105440.056852.1513
171.5877-1.69660.06242.2691-0.07221.1472-0.03680.35870.3574-0.1357-0.24120.1944-0.4402-0.24250.19870.34410.0108-0.10250.2122-0.00910.2869-15.794132.800430.7544
181.0429-0.7184-0.66752.32211.29571.3317-0.21570.11630.18520.2454-0.15170.2901-0.3186-0.32340.29860.39210.0419-0.04540.2274-0.03870.2804-16.177431.301231.0507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 217 )
3X-RAY DIFFRACTION3chain 'A' and (resid 218 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 275 )
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 314 )
6X-RAY DIFFRACTION6chain 'A' and (resid 315 through 340 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'B' and (resid 164 through 176 )
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 192 )
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 217 )
12X-RAY DIFFRACTION12chain 'B' and (resid 218 through 239 )
13X-RAY DIFFRACTION13chain 'B' and (resid 240 through 286 )
14X-RAY DIFFRACTION14chain 'B' and (resid 287 through 314 )
15X-RAY DIFFRACTION15chain 'B' and (resid 315 through 328 )
16X-RAY DIFFRACTION16chain 'B' and (resid 329 through 340 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 10 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 10 )

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