[English] 日本語
Yorodumi
- PDB-7cd5: mAPE1-blunt-ended dsDNA product complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cd5
TitlemAPE1-blunt-ended dsDNA product complex
Components
  • DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-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 / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair ...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 / 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 / negative regulation of smooth muscle cell migration / DNA-(abasic site) binding / : / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / phosphoric diester hydrolase activity / DNA demethylation / cellular response to peptide hormone stimulus / NF-kappaB binding / positive regulation of G1/S transition of mitotic cell cycle / cellular response to cAMP / RNA endonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / regulation of mRNA stability / telomere maintenance / cell redox homeostasis / base-excision repair / chromatin DNA binding / cellular response to hydrogen peroxide / regulation of apoptotic process / DNA recombination / transcription regulator complex / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / nuclear speck / response to xenobiotic stimulus / DNA repair / centrosome / protein-containing complex binding / 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-(apurinic or apyrimidinic site) endonuclease
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,8352
Polymers41,8352
Non-polymers00
Water0
1
B: DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3')
A: DNA-(apurinic or apyrimidinic site) endonuclease

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


Theoretical massNumber of molelcules
Total (without water)83,6704
Polymers83,6704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)107.210, 107.210, 230.792
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: DNA chain DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3')


Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DNA-(apurinic or apyrimidinic site) endonuclease / APEX nuclease / APEN / Apurinic-apyrimidinic endonuclease 1 / AP endonuclease 1 / REF-1 / Redox factor-1


Mass: 39095.336 Da / Num. of mol.: 1
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 25% v/v Polyethylene glycol 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 22366 / % possible obs: 99.5 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.02 / Rrim(I) all: 0.093 / Χ2: 1.112 / Net I/σ(I): 8.4 / Num. measured all: 431037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.813.60.49920610.9380.1330.5170.53494.9
2.8-2.9116.40.46821990.9610.1170.4830.55100
2.91-3.0417.60.39821830.9790.0950.4090.598100
3.04-3.218.80.26722060.9940.0620.2740.71100
3.2-3.420.10.17122040.9980.0380.1750.822100
3.4-3.6620.70.1322240.9980.0290.1330.96699.9
3.66-4.0321.30.09422440.9990.020.0961.067100
4.03-4.6121.80.07222590.9990.0150.0731.297100
4.61-5.821.30.08223090.9990.0180.0842.237100
5.8-3020.40.044247710.010.0451.68699.9

-
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: 2.7→29.892 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 1669 7.49 %
Rwork0.1889 20607 -
obs0.191 22276 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151 Å2 / Biso mean: 65.2002 Å2 / Biso min: 32.07 Å2
Refinement stepCycle: final / Resolution: 2.7→29.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 160 0 0 2374
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 (%)
2.7002-2.77960.31271260.3127165499
2.7796-2.86920.3471390.29641676100
2.8692-2.97170.3171530.26671669100
2.9717-3.09050.31231230.25941689100
3.0905-3.2310.26021300.22261690100
3.231-3.40110.2231400.20921679100
3.4011-3.61390.23161350.19651717100
3.6139-3.89240.20151540.17141689100
3.8924-4.28310.16971360.16031723100
4.2831-4.90050.15691500.14231740100
4.9005-6.16520.18671330.16941777100
6.1652-29.8920.22561500.18031904100
Refinement TLS params.Method: refined / Origin x: 49.5976 Å / Origin y: -21.7264 Å / Origin z: -0.389 Å
111213212223313233
T0.3351 Å2-0.0362 Å2-0.0274 Å2-0.3787 Å20.0636 Å2--0.3668 Å2
L0.4532 °20.0899 °2-0.0505 °2-1.9249 °20.469 °2--0.8514 °2
S0.0991 Å °0.0492 Å °0.0166 Å °-0.0228 Å °-0.1933 Å °-0.0175 Å °-0.1484 Å °-0.1386 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 8
2X-RAY DIFFRACTION1allA40 - 317

+
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