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- PDB-6bow: Human APE1 substrate complex with an T/T mismatch adjacent the THF -

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Basic information

Entry
Database: PDB / ID: 6bow
TitleHuman APE1 substrate complex with an T/T mismatch adjacent the THF
Components
  • (21-mer DNA) x 2
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsDNA BINDING PROTEIN/DNA / HYDROLASE LYASE / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / double-stranded telomeric DNA binding ...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 DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / double-stranded telomeric DNA binding / 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / 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. / 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: 1.59 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M. / Fairlamb, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024431 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Authors: Fairlamb, M.S. / Whitaker, A.M. / Freudenthal, B.D.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA


Theoretical massNumber of molelcules
Total (without water)83,9204
Polymers83,9204
Non-polymers00
Water9,440524
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA


Theoretical massNumber of molelcules
Total (without water)48,3463
Polymers48,3463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-23 kcal/mol
Surface area17670 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase


Theoretical massNumber of molelcules
Total (without water)35,5741
Polymers35,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.259, 61.333, 73.119
Angle α, β, γ (deg.)83.31, 78.28, 86.96
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 35574.426 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 21-mer DNA


Mass: 6347.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 21-mer DNA


Mass: 6424.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Mosaicity: 1.175 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.591→25 Å / Num. obs: 190771 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.508 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 1.59→24.56 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 3847 2.02 %
Rwork0.214 --
obs0.214 190771 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 846 0 524 5551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125313
X-RAY DIFFRACTIONf_angle_d1.2737380
X-RAY DIFFRACTIONf_dihedral_angle_d19.4813043
X-RAY DIFFRACTIONf_chiral_restr0.069801
X-RAY DIFFRACTIONf_plane_restr0.009801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5908-1.61090.40331070.32855178X-RAY DIFFRACTION71
1.6109-1.63210.32941350.31556632X-RAY DIFFRACTION90
1.6321-1.65450.2781420.30176735X-RAY DIFFRACTION92
1.6545-1.67810.33791370.30236668X-RAY DIFFRACTION93
1.6781-1.70310.31431420.30766892X-RAY DIFFRACTION93
1.7031-1.72980.29691360.3076747X-RAY DIFFRACTION94
1.7298-1.75810.38051470.31526996X-RAY DIFFRACTION95
1.7581-1.78840.39881360.31256844X-RAY DIFFRACTION94
1.7884-1.82090.33241430.32586970X-RAY DIFFRACTION96
1.8209-1.85590.33851450.34066989X-RAY DIFFRACTION96
1.8559-1.89380.35551390.33386782X-RAY DIFFRACTION93
1.8938-1.9350.34061480.27646998X-RAY DIFFRACTION95
1.935-1.980.32821370.28386964X-RAY DIFFRACTION96
1.98-2.02940.32831440.2667129X-RAY DIFFRACTION98
2.0294-2.08430.23171420.23597013X-RAY DIFFRACTION97
2.0843-2.14560.23481500.23247172X-RAY DIFFRACTION98
2.1456-2.21480.23661520.24287198X-RAY DIFFRACTION98
2.2148-2.29390.32631410.24236921X-RAY DIFFRACTION96
2.2939-2.38570.30541480.25427034X-RAY DIFFRACTION97
2.3857-2.49420.2831440.24627110X-RAY DIFFRACTION97
2.4942-2.62550.31651450.23457055X-RAY DIFFRACTION97
2.6255-2.78980.2091470.21597069X-RAY DIFFRACTION97
2.7898-3.00480.25351460.21777020X-RAY DIFFRACTION97
3.0048-3.30660.24781460.1967146X-RAY DIFFRACTION98
3.3066-3.78360.1631520.17257217X-RAY DIFFRACTION99
3.7836-4.76120.17891470.15137222X-RAY DIFFRACTION99
4.7612-24.56430.17761490.15917223X-RAY DIFFRACTION99

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