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- PDB-7tr7: APE1 product complex with abasic ssDNA -

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Basic information

Entry
Database: PDB / ID: 7tr7
TitleAPE1 product complex with abasic ssDNA
Components
  • DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE/DNA / DNA Repair / Abasic ssDNA / AP-Endonuclease / LYASE / LYASE-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 / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease 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 / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / 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 / nucleus / metal ion binding / 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 repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFreudenthal, B.D. / Hoitsma, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES029203 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics.
Authors: Hoitsma, N.M. / Norris, J. / Khoang, T.H. / Kaushik, V. / Chadda, R. / Antony, E. / Hedglin, M. / Freudenthal, B.D.
History
DepositionJan 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 2, 2023Group: 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 25, 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
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase
D: DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')
C: DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3406
Polymers66,2924
Non-polymers492
Water6,413356
1
A: DNA-(apurinic or apyrimidinic site) lyase
D: DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1703
Polymers33,1462
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-17 kcal/mol
Surface area13190 Å2
MethodPISA
2
C: DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')
hetero molecules

B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)33,1703
Polymers33,1462
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+y+1,-x,z+1/31
Buried area1380 Å2
ΔGint-16 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.717, 83.717, 204.179
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) lyase / APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31156.477 Da / Num. of mol.: 2 / Mutation: C138A
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
#2: DNA chain DNA (5'-D(P*(3DR)P*CP*GP*AP*TP*GP*C)-3')


Mass: 1989.313 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 3.12 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05M KCl, 0.05M sodium cacodylate pH 6, 10% PEG 8,000, 5mM spermine, 5mM L-Argininamide dihydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 83056 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.64 Å2 / Rrim(I) all: 0.08 / Net I/σ(I): 20.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.3 % / Num. unique obs: 2717 / CC1/2: 0.759 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 2→24.81 Å / SU ML: 0.2122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2147 3035 3.65 %
Rwork0.1821 80021 -
obs0.1834 83056 76.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.45 Å2
Refinement stepCycle: LAST / Resolution: 2→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 270 2 356 5004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01094851
X-RAY DIFFRACTIONf_angle_d1.08776654
X-RAY DIFFRACTIONf_chiral_restr0.0626707
X-RAY DIFFRACTIONf_plane_restr0.0057809
X-RAY DIFFRACTIONf_dihedral_angle_d22.31811825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.2917860.26892291X-RAY DIFFRACTION48.58
2.03-2.060.3075920.24592321X-RAY DIFFRACTION49.22
2.06-2.10.288860.24722403X-RAY DIFFRACTION50.36
2.1-2.140.2773920.24482440X-RAY DIFFRACTION51.45
2.14-2.180.24571000.24032512X-RAY DIFFRACTION53.39
2.18-2.220.24641030.23572600X-RAY DIFFRACTION55.34
2.22-2.270.34521050.22652831X-RAY DIFFRACTION59.3
2.27-2.320.261210.21813110X-RAY DIFFRACTION65.54
2.33-2.380.29341330.21833447X-RAY DIFFRACTION73.03
2.38-2.450.28231450.20723892X-RAY DIFFRACTION82.14
2.45-2.520.23351640.22164031X-RAY DIFFRACTION85.93
2.52-2.60.24041600.21114175X-RAY DIFFRACTION87.91
2.6-2.690.23591520.20084208X-RAY DIFFRACTION88.33
2.69-2.80.20591480.2124196X-RAY DIFFRACTION89.09
2.8-2.930.26831610.19774255X-RAY DIFFRACTION90.03
2.93-3.080.32941540.20274367X-RAY DIFFRACTION90.86
3.08-3.270.19931710.18794260X-RAY DIFFRACTION91.55
3.28-3.530.16661700.17184433X-RAY DIFFRACTION93.31
3.53-3.880.20031730.16344526X-RAY DIFFRACTION95.64
3.88-4.440.17651700.14174541X-RAY DIFFRACTION95.77
4.44-5.580.14731800.14024569X-RAY DIFFRACTION96.29
5.59-24.810.17921690.14614613X-RAY DIFFRACTION97.83

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