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- PDB-5wn3: APE1 F266A exonuclease substrate complex with a C/T mismatch -

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Basic information

Entry
Database: PDB / ID: 5wn3
TitleAPE1 F266A exonuclease substrate complex with a C/T mismatch
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DV3))-3')
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*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 / LYASE/DNA / LYASE-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: 2 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024431 United States
CitationJournal: Nat Commun / Year: 2018
Title: Molecular snapshots of APE1 proofreading mismatches and removing DNA damage.
Authors: Whitaker, A.M. / Flynn, T.S. / Freudenthal, B.D.
History
DepositionJul 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 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 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 4, 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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: 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*(DV3))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
A: DNA-(apurinic or apyrimidinic site) lyase
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,42415
Polymers74,9965
Non-polymers42810
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*(DV3))-3')
E: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1269
Polymers43,9164
Non-polymers2105
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-43 kcal/mol
Surface area18010 Å2
MethodPISA
2
A: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2986
Polymers31,0801
Non-polymers2185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-26 kcal/mol
Surface area12480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.144, 65.545, 91.441
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules CDE

#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*(DV3))-3')


Mass: 3077.070 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*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


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 / APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / APE-1 / REF-1 / Redox factor-1


Mass: 31080.379 Da / Num. of mol.: 2 / Mutation: C138A, F266A
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 BL21 (DE3) (bacteria)
References: UniProt: P27695, Hydrolases; Acting on ester bonds, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 5 types, 253 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.68 Å3/Da / Density % sol: 54.13 % / Mosaicity: 1.074 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride

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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: Jun 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.99→25 Å / Num. obs: 53955 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 32.42 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.892 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5DFF

5dff


Resolution: 2→24.76 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.43
RfactorNum. reflection% reflection
Rfree0.258 1975 3.7 %
Rwork0.21 --
obs0.211 53376 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 41.79 Å2
Refinement stepCycle: LAST / Resolution: 2→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 854 22 243 5482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115583
X-RAY DIFFRACTIONf_angle_d1.2987761
X-RAY DIFFRACTIONf_dihedral_angle_d21.5593200
X-RAY DIFFRACTIONf_chiral_restr0.067827
X-RAY DIFFRACTIONf_plane_restr0.007842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9911-2.04090.33841370.29983386X-RAY DIFFRACTION91
2.0409-2.0960.30531370.26893693X-RAY DIFFRACTION99
2.096-2.15770.29521410.25233725X-RAY DIFFRACTION100
2.1577-2.22730.34841540.25293664X-RAY DIFFRACTION100
2.2273-2.30680.32931370.29133707X-RAY DIFFRACTION99
2.3068-2.39910.37961410.28193666X-RAY DIFFRACTION99
2.3991-2.50820.32881380.26283675X-RAY DIFFRACTION99
2.5082-2.64030.33891430.2663677X-RAY DIFFRACTION98
2.6403-2.80550.37061380.26153623X-RAY DIFFRACTION97
2.8055-3.02170.3161340.25283579X-RAY DIFFRACTION96
3.0217-3.32520.22891430.21553659X-RAY DIFFRACTION98
3.3252-3.80490.23031520.17253763X-RAY DIFFRACTION100
3.8049-4.7880.19491390.15953740X-RAY DIFFRACTION99
4.788-24.76350.20351410.16983844X-RAY DIFFRACTION100

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