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- PDB-6w3l: APE1 exonuclease substrate complex wild-type -

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Basic information

Entry
Database: PDB / ID: 6w3l
TitleAPE1 exonuclease substrate complex wild-type
Components
  • DNA-(apurinic or apyrimidinic site) lyase
  • GCTGATGCG(C7R)
  • 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) / 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: 2.59 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: TCGACGGATCC
D: GCTGATGCG(C7R)
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)75,3619
Polymers75,2125
Non-polymers1484
Water1,802100
1
C: TCGACGGATCC
D: GCTGATGCG(C7R)
E: GGATCCGTCGATCGCATCAGC
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0876
Polymers44,0244
Non-polymers632
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-38 kcal/mol
Surface area17760 Å2
MethodPISA
2
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2743
Polymers31,1891
Non-polymers852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-18 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.371, 65.196, 91.258
Angle α, β, γ (deg.)90.000, 110.267, 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 GCTGATGCG(C7R)


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 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31188.539 Da / Num. of mol.: 2
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 , 4 types, 104 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
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 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.59→24.77 Å / Num. obs: 44162 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 60.64 Å2 / Rrim(I) all: 0.123 / Net I/σ(I): 12.2
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 2112 / CC1/2: 0.714 / Rrim(I) all: 1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data scaling
PHENIX1.17.1_3660phasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WN4

5wn4


Resolution: 2.59→24.77 Å / SU ML: 0.4954 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.5933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277 3612 8.33 %
Rwork0.217 39749 -
obs0.2221 43361 89.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.25 Å2
Refinement stepCycle: LAST / Resolution: 2.59→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 854 7 100 5335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01665477
X-RAY DIFFRACTIONf_angle_d1.50247607
X-RAY DIFFRACTIONf_chiral_restr0.0898815
X-RAY DIFFRACTIONf_plane_restr0.0082839
X-RAY DIFFRACTIONf_dihedral_angle_d26.03242076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.620.4141170.34891055X-RAY DIFFRACTION60.38
2.62-2.660.43561250.34541433X-RAY DIFFRACTION85.89
2.66-2.690.43371430.34191470X-RAY DIFFRACTION86.95
2.69-2.730.35781350.31511517X-RAY DIFFRACTION87.87
2.73-2.780.37381330.31721484X-RAY DIFFRACTION89.19
2.78-2.820.37931350.32041502X-RAY DIFFRACTION88.77
2.82-2.870.36831320.33481540X-RAY DIFFRACTION88.79
2.87-2.920.51271420.38611510X-RAY DIFFRACTION88.96
2.92-2.980.52851390.35261498X-RAY DIFFRACTION88.82
2.98-3.040.39981410.33131567X-RAY DIFFRACTION90.66
3.04-3.110.39571240.31281545X-RAY DIFFRACTION89.59
3.11-3.180.42311430.26931485X-RAY DIFFRACTION91.31
3.18-3.260.30041570.26271600X-RAY DIFFRACTION92.13
3.26-3.340.32521430.26821534X-RAY DIFFRACTION92.86
3.34-3.440.33671390.23831614X-RAY DIFFRACTION93.74
3.44-3.550.29871310.21541625X-RAY DIFFRACTION94.77
3.55-3.680.27111530.22061586X-RAY DIFFRACTION94.56
3.68-3.830.2781380.21061596X-RAY DIFFRACTION91.5
3.83-40.28121380.21533X-RAY DIFFRACTION90.72
4-4.210.28291370.19241507X-RAY DIFFRACTION89.98
4.21-4.470.19051380.17491556X-RAY DIFFRACTION90.25
4.47-4.810.24411430.171547X-RAY DIFFRACTION91.2
4.82-5.30.22431430.17391592X-RAY DIFFRACTION94.24
5.3-6.050.22871470.1771619X-RAY DIFFRACTION94.59
6.06-7.590.20851410.18731617X-RAY DIFFRACTION95.34
7.59-24.770.18811550.14571617X-RAY DIFFRACTION95.47

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