[English] 日本語
Yorodumi
- PDB-6w4t: APE1 Y269A phosphorothioate substrate complex with abasic DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w4t
TitleAPE1 Y269A phosphorothioate substrate complex with abasic DNA
Components
  • DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsLYASE/DNA / DNA Repair / AP-Endonuclease / DNA Binding / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / 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 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsFreudenthal, B.D. / Hoitsma, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES029203 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.
Authors: Hoitsma, N.M. / Whitaker, A.M. / Beckwitt, E.C. / Jang, S. / Agarwal, P.K. / Van Houten, B. / Freudenthal, B.D.
History
DepositionMar 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 18, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-(apurinic or apyrimidinic site) lyase
P: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
V: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)87,7216
Polymers87,7216
Non-polymers00
Water70339
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
V: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8613
Polymers43,8613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-21 kcal/mol
Surface area17480 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
C: DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)43,8613
Polymers43,8613
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-18 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.659, 148.315, 153.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 31064.379 Da / Num. of mol.: 2 / Mutation: Y269A, C138A
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
#2: DNA chain DNA (5'-D(P*GP*CP*TP*GP*AP*TP*GP*CP*GP*TP*(48Z)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')


Mass: 6347.127 Da / Num. of mol.: 2 / 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*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 6449.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→48.29 Å / Num. obs: 27446 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 56.88 Å2 / Rrim(I) all: 0.261 / Net I/σ(I): 7.4
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 6.8 % / Num. unique obs: 3910 / CC1/2: 0.395 / Rrim(I) all: 2.67 / % possible all: 100

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.17.1_3660refinement
Blu-Icedata collection
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 2.77→48.29 Å / SU ML: 0.5252 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.4919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 1267 4.69 %
Rwork0.2214 25759 -
obs0.224 27026 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.9 Å2
Refinement stepCycle: LAST / Resolution: 2.77→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 1691 0 39 6110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01756407
X-RAY DIFFRACTIONf_angle_d1.43169025
X-RAY DIFFRACTIONf_chiral_restr0.0891976
X-RAY DIFFRACTIONf_plane_restr0.0082874
X-RAY DIFFRACTIONf_dihedral_angle_d28.85912478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.880.44781390.39172560X-RAY DIFFRACTION90.39
2.88-3.010.43461260.34142832X-RAY DIFFRACTION99.13
3.01-3.170.34461360.27542837X-RAY DIFFRACTION99.83
3.17-3.370.26231270.24282871X-RAY DIFFRACTION99.6
3.37-3.630.34491520.23982855X-RAY DIFFRACTION99.73
3.63-40.27621400.21632874X-RAY DIFFRACTION99.97
4-4.570.24271650.19112894X-RAY DIFFRACTION99.74
4.57-5.760.24811320.1912957X-RAY DIFFRACTION99.84
5.76-48.290.20961500.18183079X-RAY DIFFRACTION99.75

+
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://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