[English] 日本語
Yorodumi
- PDB-9dp4: APE1 N174Q Product Complex with Abasic DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dp4
TitleAPE1 N174Q Product Complex with Abasic DNA
Components
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA repair nuclease/redox regulator APEX1
KeywordsHYDROLASE/DNA / APE1 / APEX1 / Endonuclease / DNA Repair / HYDROLASE-DNA complex
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 / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III ...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 / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphodiesterase I activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 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 / base-excision repair, gap-filling / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / regulation of apoptotic process / DNA recombination / damaged DNA binding / chromosome, telomeric region / 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
DI(HYDROXYETHYL)ETHER / 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: 2.25 Å
AuthorsDeHart, K.D. / Hoitsma, N.M. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES029203 United States
CitationJournal: To Be Published
Title: N174 Physically and Chemically Stabilizes the APE1 Endonuclease Reaction
Authors: DeHart, K.D. / Hoitsma, N.M. / Thompson, S.H. / Freudenthal, B.D.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA repair nuclease/redox regulator APEX1
B: DNA repair nuclease/redox regulator APEX1
D: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
E: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
G: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
H: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
I: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,07412
Polymers87,8148
Non-polymers2614
Water4,486249
1
A: DNA repair nuclease/redox regulator APEX1
D: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
E: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0376
Polymers43,9074
Non-polymers1302
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-33 kcal/mol
Surface area17220 Å2
MethodPISA
2
B: DNA repair nuclease/redox regulator APEX1
G: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
H: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
I: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0376
Polymers43,9074
Non-polymers1302
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-24 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.423, 153.423, 45.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA repair nuclease/redox regulator APEX1 / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / AP endonuclease 1 / APE-1 / DNA- ...APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / AP endonuclease 1 / APE-1 / DNA-(apurinic or apyrimidinic site) endonuclease / Redox factor-1 / REF-1


Mass: 31170.504 Da / Num. of mol.: 2 / Mutation: tr1-42, C138A, N174Q
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, exodeoxyribonuclease III, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters

-
DNA chain , 3 types, 6 molecules DGEHFI

#2: DNA chain DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Mass: 3210.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 3061.004 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6465.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 253 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES free acid, 200 mM ammonium acetate, 25% PEG3350

-
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: Feb 12, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→48.52 Å / Num. obs: 63992 / % possible obs: 98.5 % / Redundancy: 5.6 % / Rrim(I) all: 0.1 / Net I/σ(I): 13.74
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 2206 / CC1/2: 0.616 / CC star: 0.873 / % possible all: 86.7

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000705cdata collection
HKL-3000705cdata reduction
HKL-3000705cdata scaling
PHENIX1.19.2-4158-000phasing
Coot0.9model building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.52 Å / Cross valid method: FREE R-VALUE / σ(F): 13.36 / Phase error: 26.8 / Stereochemistry target values: TWIN_LSQ_F / Details: Twinning Present. Operator applied: h,-k,-l
RfactorNum. reflection% reflection
Rfree0.2485 3862 6.04 %
Rwork0.2152 --
obs0.2208 63992 65.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 1698 16 249 6340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136417
X-RAY DIFFRACTIONf_angle_d1.8169050
X-RAY DIFFRACTIONf_dihedral_angle_d26.632499
X-RAY DIFFRACTIONf_chiral_restr0.118975
X-RAY DIFFRACTIONf_plane_restr0.008879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.2024250.2718513X-RAY DIFFRACTION10
2.29-2.330.2274340.2832592X-RAY DIFFRACTION12
2.33-2.380.2092390.2914728X-RAY DIFFRACTION15
2.38-2.430.4301350.2987797X-RAY DIFFRACTION17
2.43-2.480.4263520.31261015X-RAY DIFFRACTION21
2.48-2.540.3123650.32081312X-RAY DIFFRACTION27
2.54-2.60.3271030.30641859X-RAY DIFFRACTION39
2.6-2.670.37751210.3012438X-RAY DIFFRACTION49
2.67-2.750.31851530.30052893X-RAY DIFFRACTION60
2.75-2.840.38891820.28283527X-RAY DIFFRACTION71
2.84-2.940.38412060.2813984X-RAY DIFFRACTION82
2.94-3.060.35692280.29064359X-RAY DIFFRACTION89
3.06-3.20.24562390.23844516X-RAY DIFFRACTION92
3.2-3.370.25622470.21854536X-RAY DIFFRACTION93
3.37-3.580.26322450.21674648X-RAY DIFFRACTION95
3.58-3.850.24312620.18974590X-RAY DIFFRACTION95
3.85-4.240.20722570.18474665X-RAY DIFFRACTION95
4.24-4.850.18472410.17784618X-RAY DIFFRACTION95
4.85-6.110.21672550.19574625X-RAY DIFFRACTION95
6.11-48.520.22862340.2034554X-RAY DIFFRACTION93

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more