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- PDB-6w3n: APE1 exonuclease substrate complex D148E -

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Basic information

Entry
Database: PDB / ID: 6w3n
TitleAPE1 exonuclease substrate complex D148E
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3')
  • DNA-(apurinic or apyrimidinic site) lyaseDNA-(apurinic or apyrimidinic site) lyase
  • GGATCCGTCGATCGCATCAGC
  • TCGACGGATCC
KeywordsDNA BINDING PROTEIN/DNA / nuclease / abasic site / DNA repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / phosphodiesterase I activity / exodeoxyribonuclease III / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / : / uracil DNA N-glycosylase activity / DNA catabolic process / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / regulation of apoptotic process / DNA recombination / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase ...AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01-ES029203 United States
American Cancer SocietyPF-1815401-DMC United States
CitationJournal: DNA Repair (Amst.) / Year: 2020
Title: Molecular and structural characterization of disease-associated APE1 polymorphisms.
Authors: Whitaker, A.M. / Stark, W.J. / Flynn, T.S. / Freudenthal, B.D.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
C: TCGACGGATCC
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3')
E: GGATCCGTCGATCGCATCAGC
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3437
Polymers75,2415
Non-polymers1022
Water75742
1
C: TCGACGGATCC
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3')
E: GGATCCGTCGATCGCATCAGC
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0785
Polymers44,0384
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-31 kcal/mol
Surface area17950 Å2
MethodPISA
2
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2652
Polymers31,2031
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint2 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.554, 65.074, 91.424
Angle α, β, γ (deg.)90.000, 109.928, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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DNA chain , 3 types, 3 molecules CDE

#1: DNA chain TCGACGGATCC


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3')


Mass: 3077.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain GGATCCGTCGATCGCATCAGC


Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules AB

#4: Protein DNA-(apurinic or apyrimidinic site) lyase / DNA-(apurinic or apyrimidinic site) lyase / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31202.566 Da / Num. of mol.: 2 / Mutation: D148E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1 / Production host: Escherichia coli (E. coli)
References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 3 types, 44 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→25 Å / Num. obs: 37101 / % possible obs: 96.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 57.27 Å2 / Rrim(I) all: 0.21 / Net I/σ(I): 7.8
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 1645 / CC1/2: 0.714 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W4N

5w4n


Resolution: 2.69→24.76 Å / SU ML: 0.5056 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.7295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3084 3467 9.55 %
Rwork0.2491 32845 -
obs0.2549 36312 84.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.64 Å2
Refinement stepCycle: LAST / Resolution: 2.69→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 835 5 42 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01225422
X-RAY DIFFRACTIONf_angle_d1.35887527
X-RAY DIFFRACTIONf_chiral_restr0.2671808
X-RAY DIFFRACTIONf_plane_restr0.008830
X-RAY DIFFRACTIONf_dihedral_angle_d26.82842066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.730.44641000.3752868X-RAY DIFFRACTION56.34
2.73-2.770.42531280.38151130X-RAY DIFFRACTION72.8
2.77-2.810.42941240.36461249X-RAY DIFFRACTION79.73
2.81-2.850.46131290.34161222X-RAY DIFFRACTION79.1
2.85-2.90.42281230.33741200X-RAY DIFFRACTION78.33
2.9-2.950.35481360.33081284X-RAY DIFFRACTION80.27
2.95-30.41461250.36051176X-RAY DIFFRACTION79.18
3-3.060.46371290.40781336X-RAY DIFFRACTION83.43
3.06-3.120.47311460.38311335X-RAY DIFFRACTION86.1
3.12-3.190.41681500.32071313X-RAY DIFFRACTION86.01
3.19-3.260.43241280.28681406X-RAY DIFFRACTION88.31
3.26-3.350.36881500.28431339X-RAY DIFFRACTION87.03
3.35-3.440.35981350.27371392X-RAY DIFFRACTION88.99
3.44-3.540.31781350.2631409X-RAY DIFFRACTION88.74
3.54-3.650.31011400.26191386X-RAY DIFFRACTION89.55
3.65-3.780.2971610.2471347X-RAY DIFFRACTION88.29
3.78-3.930.30621450.24421324X-RAY DIFFRACTION86.62
3.93-4.110.30131360.23591376X-RAY DIFFRACTION87.45
4.11-4.330.3021590.23111349X-RAY DIFFRACTION86.72
4.33-4.60.2751540.20231368X-RAY DIFFRACTION88.9
4.6-4.950.2581360.2061390X-RAY DIFFRACTION89.34
4.95-5.440.29671530.21481420X-RAY DIFFRACTION91.35
5.44-6.220.19491560.20611402X-RAY DIFFRACTION91.32
6.22-7.790.25911510.22391409X-RAY DIFFRACTION90.86
7.79-24.760.21361380.17041415X-RAY DIFFRACTION90.19

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