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- PDB-6bor: Human APE1 substrate complex with an G/G mismatch adjacent the THF -

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Basic information

Entry
Database: PDB / ID: 6bor
TitleHuman APE1 substrate complex with an G/G 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 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. / 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: 1.84 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2989
Polymers84,0144
Non-polymers2845
Water10,160564
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6317
Polymers48,4103
Non-polymers2224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-20 kcal/mol
Surface area17560 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6672
Polymers35,6051
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint5 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.408, 60.204, 73.014
Angle α, β, γ (deg.)82.940, 80.290, 89.100
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35604.520 Da / Num. of mol.: 2 / Mutation: E96Q, 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

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DNA chain , 2 types, 2 molecules PV

#2: DNA chain 21-mer DNA


Mass: 6356.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 21-mer DNA


Mass: 6449.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 569 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 2.27 Å3/Da / Density % sol: 45.88 % / Mosaicity: 1.141 °
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: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. obs: 115113 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.07 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Χ2: 1.629 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.882.20.50531230.0990.4220.6611.97697
1.88-1.922.20.58230800.4680.4880.7632.66397.6
1.92-1.952.30.42731500.0570.3550.5582.40897.8
1.95-1.992.40.30631460.5540.2380.3891.65398.4
1.99-2.042.50.23731830.8940.1770.2971.34199.2
2.04-2.082.70.31231800.8960.2240.3863.56298.9
2.08-2.142.90.21731840.4480.1530.2672.07599.6
2.14-2.193.10.19231600.940.1250.231.77799.9
2.19-2.263.50.23432060.3530.1480.2782.24999.9
2.26-2.333.80.19332250.8160.1120.2242.0799.9
2.33-2.414.20.14931630.9740.0820.1711.641100
2.41-2.514.70.13532250.9830.0690.1521.589100
2.51-2.625.50.12832080.9870.060.1421.604100
2.62-2.765.90.10731740.9880.0480.1181.487100
2.76-2.9460.08931860.9940.040.0981.367100
2.94-3.1660.07632120.9950.0340.0841.441100
3.16-3.4860.06731880.9960.030.0731.382100
3.48-3.985.90.0631950.9930.0270.0661.372100
3.98-5.015.90.05232170.9970.0240.0571.119100
5.01-255.60.05431830.9960.0250.0591.379100

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Processing

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

5dff


Resolution: 1.84→24.811 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2092 3621 3.15 %
Rwork0.1703 --
obs0.1715 115113 89.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.7 Å2 / Biso mean: 22.2407 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.84→24.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 849 17 564 5713
Biso mean--21.95 29.03 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155398
X-RAY DIFFRACTIONf_angle_d1.4487502
X-RAY DIFFRACTIONf_chiral_restr0.082809
X-RAY DIFFRACTIONf_plane_restr0.009820
X-RAY DIFFRACTIONf_dihedral_angle_d19.1813079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86420.30921060.29293344345070
1.8642-1.88970.2831200.26983581370176
1.8897-1.91670.26771260.23983720384677
1.9167-1.94530.26391260.22253751387779
1.9453-1.97570.28491240.21863817394181
1.9757-2.00810.24651270.21364030415782
2.0081-2.04270.23051220.21033937405983
2.0427-2.07980.25091330.20964009414283
2.0798-2.11980.29741300.2044118424887
2.1198-2.1630.25061390.19394138427788
2.163-2.21010.28041390.19384299443889
2.2101-2.26140.23471360.1824228436490
2.2614-2.31790.2381470.1894464461191
2.3179-2.38060.25331380.18064332447093
2.3806-2.45060.26191440.1864531467594
2.4506-2.52960.25641490.17484499464895
2.5296-2.61990.22351500.1774664481496
2.6199-2.72470.2461490.1744562471196
2.7247-2.84850.20941500.17274659480997
2.8485-2.99840.21931500.18334649479997
2.9984-3.18590.19451490.17414668481798
3.1859-3.43130.16661540.15164683483798
3.4313-3.77560.18921540.14684677483198
3.7756-4.31940.17351500.1354703485398
4.3194-5.43260.15011550.12884718487399
5.4326-24.81280.1531540.14144711486598

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