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- PDB-7tc3: Human APE1 in the apo form -

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Basic information

Entry
Database: PDB / ID: 7tc3
TitleHuman APE1 in the apo form
ComponentsDNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial
KeywordsHYDROLASE / AP Endonuclease1 / APE1
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease 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 / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / 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 / nucleus / metal ion binding / 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 repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.252 Å
AuthorsPidugu, L.S. / Pozharski, E. / Drohat, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM072711, R35-GM136225 United States
CitationJournal: Plos One / Year: 2023
Title: Characterizing inhibitors of human AP endonuclease 1.
Authors: Pidugu, L.S. / Servius, H.W. / Sevdalis, S.E. / Cook, M.E. / Varney, K.M. / Pozharski, E. / Drohat, A.C.
History
DepositionDec 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4116
Polymers32,1001
Non-polymers3105
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.651, 141.442, 45.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-615-

HOH

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Components

#1: Protein DNA-(apurinic or apyrimidinic site) endonuclease, mitochondrial


Mass: 32100.492 Da / Num. of mol.: 1
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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2017
RadiationMonochromator: Single crystal, cylindrically bent Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.25→38.942 Å / Num. obs: 82613 / % possible obs: 98.9 % / Redundancy: 10.8 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Rrim(I) all: 0.046 / Net I/σ(I): 22.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.25-1.271.71.484533531910.1661.2221.9350.578.9
6.86-38.9411.30.024692361510.0070.02575.499.6

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Processing

Software
NameVersionClassification
PHENIXdev_3409refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LND

4lnd


Resolution: 1.252→38.942 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1779 4098 4.99 %
Rwork0.1511 78067 -
obs0.1524 82165 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.75 Å2 / Biso mean: 30.2559 Å2 / Biso min: 11.68 Å2
Refinement stepCycle: final / Resolution: 1.252→38.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 24 398 2611
Biso mean--50.05 50.13 -
Num. residues----282
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.252-1.26650.3909820.3735180467
1.2665-1.2820.34571360.3523249192
1.282-1.29820.34641280.3305266497
1.2982-1.31530.34181330.3116260599
1.3153-1.33330.32371600.28242734100
1.3333-1.35240.28971320.27012658100
1.3524-1.37260.24031420.23592724100
1.3726-1.3940.22741410.21322651100
1.394-1.41690.22671310.21272782100
1.4169-1.44130.2281510.20162655100
1.4413-1.46750.21871160.19222744100
1.4675-1.49570.20791300.18382713100
1.4957-1.52630.20971380.17852696100
1.5263-1.55940.17861420.17092751100
1.5594-1.59570.16591380.16492703100
1.5957-1.63560.16761360.16512706100
1.6356-1.67990.16481550.16732714100
1.6799-1.72930.19131660.15952742100
1.7293-1.78510.20941450.15852680100
1.7851-1.84890.15411330.152763100
1.8489-1.92290.16951540.14762723100
1.9229-2.01040.14881410.14692726100
2.0104-2.11640.17231450.14652760100
2.1164-2.2490.14831480.14572758100
2.249-2.42260.18591470.14362761100
2.4226-2.66640.16661300.14722801100
2.6664-3.05210.16421880.13832754100
3.0521-3.84480.16811620.1222818100
3.8448-38.9420.16551480.12582986100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3898-2.12195.23254.534-1.81286.3494-0.5489-0.9879-0.12480.50790.3605-0.1942-0.3866-0.8137-0.01490.15320.03540.020.39960.04960.324215.070519.8756-7.5825
25.1085-1.41285.44374.95520.63517.448-0.27380.87930.1626-0.6832-0.0564-0.08460.04240.18980.28310.2463-0.07510.05880.3862-0.00410.1225-3.350822.0978-29.6324
32.9932-0.52260.14852.47390.8838.0647-0.12740.09410.2397-0.12060.06180.0071-0.1608-0.25190.10090.1290.0049-0.04420.1199-0.00080.1654-10.304826.107-15.0118
41.47251.2856-1.14156.7312-1.79314.63390.157-0.59280.92820.7126-0.04280.1132-1.10.0961-0.43860.32520.0518-0.05970.2217-0.13830.3337-10.044935.6735-2.6012
53.20690.1509-0.35733.3672-0.22656.6793-0.0832-0.00850.48530.02360.06660.0006-0.4733-0.0085-0.0180.15270.0398-0.05670.1127-0.01840.2325-10.777630.976-11.0391
69.28455.1402-2.36824.9739-5.41158.84310.5124-0.41850.50520.5364-0.24251.1205-0.6957-0.2981-0.32940.36450.08920.04840.2718-0.09570.4068-19.985134.1283-0.9178
73.9097-0.3867-0.21783.12320.1984.1211-0.01230.11130.49310.06270.07120.0588-1.0577-0.4328-0.11650.29080.0809-0.0450.17860.00040.2502-20.542731.9729-10.8639
89.85566.3345-0.42358.5921-4.21855.73571.0538-2.1750.28341.8781-0.8410.673-1.5058-1.4246-0.09010.62540.0030.01380.6107-0.0360.2271-16.828522.9396.4455
94.8946-0.23820.73744.0039-0.98273.9316-0.0862-0.156-0.24050.0350.12230.40020.0993-0.3533-0.05040.10010.03990.00660.1638-0.02330.1777-21.566118.7077-7.1934
103.62423.32042.95555.81044.97654.2708-0.0761.2144-0.1889-1.16980.03970.5794-0.0957-0.64920.05260.2895-0.0088-0.06520.4084-0.0440.2663-23.843818.1304-21.4511
115.0558-2.6132.77794.3101-3.39585.7742-0.4364-0.5205-0.07870.50460.184-0.2145-0.08070.01730.24360.19870.0725-0.00580.20210.00330.1877-9.673112.2809-0.6897
124.7907-0.06534.33953.2551-2.40085.6345-0.2535-0.4141-0.68490.59680.23270.43090.42270.1059-0.06260.28430.04020.0860.220.08460.349-12.45615.8982-0.7622
138.2716-2.06184.25196.7793-1.78483.0811-0.00590.2097-0.7566-0.12940.1620.59050.3423-0.358-0.13880.2047-0.04440.02760.1711-0.03320.355-18.21625.3395-10.4147
142.2588-0.31253.59635.9764-0.42885.73050.04350.0371-0.41840.10180.03570.85330.3911-1.0311-0.14880.2091-0.10230.00710.3785-0.08170.3211-22.235310.7575-19.161
152.50490.0541-0.29861.7921-0.28721.5861-0.1478-0.0503-0.49730.01990.0608-0.18370.18780.10910.06320.13280.0304-0.00210.1244-0.01420.2599-0.25910.6158-10.9559
163.2504-3.43940.04364.13231.62815.6779-0.3613-0.47540.63090.25250.2365-0.6493-0.46540.6526-0.00250.25270.0208-0.11210.3296-0.09060.28956.673125.6037-0.1754
173.04510.41190.47581.59980.48122.6349-0.11420.1096-0.0265-0.07340.054-0.1211-0.02750.07620.04980.12250.0003-0.01080.1241-0.01790.1677-2.760720.1256-15.2617
188.4372-0.35446.30326.92671.6455.24250.02360.5475-0.3846-0.34510.17590.2241-0.131-0.7842-0.1080.1883-0.0458-0.03030.3184-0.01460.1355-12.148420.8747-26.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 36:45)A36 - 45
2X-RAY DIFFRACTION2(chain A and resid 46:58)A46 - 58
3X-RAY DIFFRACTION3(chain A and resid 59:72)A59 - 72
4X-RAY DIFFRACTION4(chain A and resid 73:77)A73 - 77
5X-RAY DIFFRACTION5(chain A and resid 78:100)A78 - 100
6X-RAY DIFFRACTION6(chain A and resid 101:107)A101 - 107
7X-RAY DIFFRACTION7(chain A and resid 108:122)A108 - 122
8X-RAY DIFFRACTION8(chain A and resid 123:128)A123 - 128
9X-RAY DIFFRACTION9(chain A and resid 129:160)A129 - 160
10X-RAY DIFFRACTION10(chain A and resid 161:165)A161 - 165
11X-RAY DIFFRACTION11(chain A and resid 166:185)A166 - 185
12X-RAY DIFFRACTION12(chain A and resid 186:189)A186 - 189
13X-RAY DIFFRACTION13(chain A and resid 190:201)A190 - 201
14X-RAY DIFFRACTION14(chain A and resid 202:206)A202 - 206
15X-RAY DIFFRACTION15(chain A and resid 207:267)A207 - 267
16X-RAY DIFFRACTION16(chain A and resid 268:272)A268 - 272
17X-RAY DIFFRACTION17(chain A and resid 273:313)A273 - 313
18X-RAY DIFFRACTION18(chain A and resid 314:318)A314 - 318

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