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- PDB-7cd6: mAPE1-recessed dsDNA product complex -

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Basic information

Entry
Database: PDB / ID: 7cd6
TitlemAPE1-recessed dsDNA product complex
Components
  • DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')
  • DNA-(apurinic or apyrimidinic site) endonuclease
KeywordsHYDROLASE/DNA / APE1 / protein-nucleic acid interaction / exonuclease / DNA repair / DNA BINDING PROTEIN / HYDROLASE-DNA complex
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / Displacement of DNA glycosylase by APEX1 / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / : ...Resolution of Abasic Sites (AP sites) / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / Displacement of DNA glycosylase by APEX1 / 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 / exodeoxyribonuclease III / double-stranded telomeric DNA binding / 3'-5'-DNA exonuclease activity / positive regulation of gene expression via chromosomal CpG island demethylation / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA catabolic process / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / cell redox homeostasis / chromatin DNA binding / regulation of apoptotic process / DNA recombination / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / 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 / 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. / 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 speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsLiu, T.C. / Hsiao, Y.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 109-2636-B-009-004 Taiwan
CitationJournal: Nat Commun / Year: 2021
Title: APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.
Authors: Liu, T.C. / Lin, C.T. / Chang, K.C. / Guo, K.W. / Wang, S. / Chu, J.W. / Hsiao, Y.Y.
History
DepositionJun 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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) endonuclease
B: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)37,4232
Polymers37,4232
Non-polymers00
Water48627
1
A: DNA-(apurinic or apyrimidinic site) endonuclease
B: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')

A: DNA-(apurinic or apyrimidinic site) endonuclease
B: DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)74,8464
Polymers74,8464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/21
Unit cell
Length a, b, c (Å)124.650, 124.650, 138.467
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 34683.359 Da / Num. of mol.: 1 / Mutation: deletion of 30 amino acids on the N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apex1, Ape, Apex, Ref1 / Production host: Escherichia coli (E. coli)
References: UniProt: P28352, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3')


Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Lithium sulfate monohydrate, 0.1M Na citrate tribasic dihydrate pH 5.5, 20% w/v Polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 6, 2018 / Details: LN2-Cooled Fixed-Exit Double
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 17975 / % possible obs: 99.9 % / Redundancy: 17 % / Biso Wilson estimate: 51.47 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.026 / Rrim(I) all: 0.116 / Χ2: 1.161 / Net I/σ(I): 7.4 / Num. measured all: 305693
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.88.90.45917330.8650.1510.4850.43399.6
2.8-2.9110.40.41317620.9410.1270.4330.45499.8
2.91-3.0412.20.36217570.9690.1040.3770.4999.9
3.04-3.214.10.28817600.990.0760.2980.57199.9
3.2-3.416.40.19117670.9980.0470.1970.71899.9
3.4-3.6618.30.152179410.0350.1560.98499.9
3.66-4.0320.20.13517780.9990.030.1391.2100
4.03-4.6122.50.09818140.9990.020.11.49399.9
4.61-5.823.50.08818440.9990.0180.0891.62399.9
5.8-3022.40.06219660.9990.0130.0631.94199.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HD7

1hd7


Resolution: 2.701→29.94 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 1434 8 %
Rwork0.1781 16480 -
obs0.1816 17914 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.47 Å2 / Biso mean: 57.5741 Å2 / Biso min: 30.15 Å2
Refinement stepCycle: final / Resolution: 2.701→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 182 0 27 2419
Biso mean---46.57 -
Num. residues----286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7012-2.79760.33491340.3156158699
2.7976-2.90960.28991420.28631617100
2.9096-3.04190.34061330.2641607100
3.0419-3.20210.31061460.24041621100
3.2021-3.40240.28781200.209163299
3.4024-3.66470.23071390.1787164999
3.6647-4.03270.19371450.15171629100
4.0327-4.61440.16661350.12641672100
4.6144-5.80670.18211640.13541680100
5.8067-29.940.18641760.15681787100
Refinement TLS params.Method: refined / Origin x: -29.8695 Å / Origin y: -35.8203 Å / Origin z: 21.0115 Å
111213212223313233
T0.336 Å20.0637 Å20.0631 Å2-0.4516 Å2-0.059 Å2--0.3549 Å2
L0.8895 °20.5027 °2-0.1206 °2-2.3244 °2-0.5106 °2--1.5754 °2
S0.104 Å °-0.0629 Å °0.0664 Å °0.0249 Å °-0.0475 Å °0.0062 Å °-0.1478 Å °-0.0708 Å °-0.0611 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA41 - 317
2X-RAY DIFFRACTION1allB1 - 9
3X-RAY DIFFRACTION1allS1 - 28

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