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- PDB-7svb: APE1 exonuclease substrate complex with 8oxoG opposite C -

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Basic information

Entry
Database: PDB / ID: 7svb
TitleAPE1 exonuclease substrate complex with 8oxoG opposite C
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsHYDROLASE/DNA / nuclease / DNA Repair protein / DNA binding protein / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III ...Resolution of Abasic Sites (AP sites) / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / Displacement of DNA glycosylase by APEX1 / 3'-5'-DNA exonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / phosphodiesterase I activity / 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 / regulation of mRNA stability / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / RNA-DNA hybrid ribonuclease activity / transcription corepressor activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / chromosome, telomeric region / oxidoreductase activity / nuclear speck / ribosome / 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. / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
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: 2.24 Å
AuthorsWhitaker, A.W. / Freudenthal, B.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)K99-ES031148 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01-ES029203 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM128562 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Processing oxidatively damaged bases at DNA strand breaks by APE1.
Authors: Whitaker, A.M. / Stark, W.J. / Freudenthal, B.D.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)75,1695
Polymers75,1695
Non-polymers00
Water4,378243
1
C: DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)44,0154
Polymers44,0154
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-26 kcal/mol
Surface area17720 Å2
MethodPISA
2
A: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)31,1551
Polymers31,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.205, 65.185, 91.330
Angle α, β, γ (deg.)90.000, 110.255, 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

#1: DNA chain DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


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*(8OG))-3')


Mass: 3117.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6409.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein DNA-(apurinic or apyrimidinic site) lyase / APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31154.504 Da / Num. of mol.: 2 / Mutation: E96Q, C138A, D210N
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7 - 14% 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: May 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.24→25 Å / Num. obs: 65243 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 35.73 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 10.1
Reflection shellResolution: 2.24→2.29 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.72 / Num. unique obs: 12091 / Rpim(I) all: 0.658 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158phasing
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dfI

5dfi


Resolution: 2.24→24.76 Å / SU ML: 0.3191 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2452 3484 5.34 %
Rwork0.1997 61759 -
obs0.2021 65243 87.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.98 Å2
Refinement stepCycle: LAST / Resolution: 2.24→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 857 0 243 5482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895481
X-RAY DIFFRACTIONf_angle_d0.99987617
X-RAY DIFFRACTIONf_chiral_restr0.0514814
X-RAY DIFFRACTIONf_plane_restr0.009841
X-RAY DIFFRACTIONf_dihedral_angle_d23.49572092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.270.37991000.351625X-RAY DIFFRACTION59.83
2.27-2.30.36421150.33451908X-RAY DIFFRACTION66.68
2.3-2.330.39021130.32731957X-RAY DIFFRACTION69.44
2.33-2.370.3743980.29972014X-RAY DIFFRACTION72.11
2.37-2.410.32371270.30062080X-RAY DIFFRACTION73.91
2.41-2.450.36031230.28872167X-RAY DIFFRACTION77.13
2.45-2.50.29071140.27592215X-RAY DIFFRACTION78.47
2.5-2.540.3331300.28112288X-RAY DIFFRACTION80.31
2.54-2.60.32961650.272331X-RAY DIFFRACTION84.52
2.6-2.650.36031210.26112447X-RAY DIFFRACTION86.99
2.65-2.710.30231400.26522488X-RAY DIFFRACTION88.84
2.71-2.780.30291290.26382558X-RAY DIFFRACTION90.11
2.78-2.860.29991540.26062606X-RAY DIFFRACTION90.94
2.86-2.940.32061620.27172577X-RAY DIFFRACTION93.23
2.94-3.040.32341430.25852655X-RAY DIFFRACTION94.15
3.04-3.140.2951470.22642656X-RAY DIFFRACTION95.96
3.14-3.270.27571530.21822813X-RAY DIFFRACTION98.41
3.27-3.420.24831500.18492789X-RAY DIFFRACTION99.63
3.42-3.60.21971570.17142838X-RAY DIFFRACTION99.63
3.6-3.820.18961630.17142785X-RAY DIFFRACTION99.46
3.82-4.120.1871570.16332783X-RAY DIFFRACTION99.29
4.12-4.530.17511470.1482780X-RAY DIFFRACTION98.99
4.53-5.180.22561520.14872789X-RAY DIFFRACTION99.19
5.18-6.50.2011620.15622822X-RAY DIFFRACTION99.87
6.5-24.760.17611620.14992788X-RAY DIFFRACTION99.49

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