[English] 日本語
Yorodumi
- PDB-6bor: Human APE1 substrate complex with an G/G mismatch adjacent the THF -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bor
TitleHuman APE1 substrate complex with an G/G mismatch adjacent the THF
Components
  • (21-mer DNA) x 2
  • DNA-(apurinic or apyrimidinic site) lyase
KeywordsDNA BINDING PROTEIN/DNA / HYDROLASE LYASE / DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / 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 / phosphodiesterase I activity ...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 / 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 / phosphodiesterase I activity / exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / phosphoric diester hydrolase activity / DNA catabolic process / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase 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 / 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. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsFreudenthal, B.D. / Whitaker, A.M. / Fairlamb, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES024431 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Authors: Fairlamb, M.S. / Whitaker, A.M. / Freudenthal, B.D.
History
DepositionNov 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
B: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2989
Polymers84,0144
Non-polymers2845
Water10,160564
1
A: DNA-(apurinic or apyrimidinic site) lyase
P: 21-mer DNA
V: 21-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6317
Polymers48,4103
Non-polymers2224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-20 kcal/mol
Surface area17560 Å2
MethodPISA
2
B: DNA-(apurinic or apyrimidinic site) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6672
Polymers35,6051
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint5 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.408, 60.204, 73.014
Angle α, β, γ (deg.)82.940, 80.290, 89.100
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 35604.520 Da / Num. of mol.: 2 / Mutation: E96Q, D210N
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

-
DNA chain , 2 types, 2 molecules PV

#2: DNA chain 21-mer DNA


Mass: 6356.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 21-mer DNA


Mass: 6449.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 569 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.88 % / Mosaicity: 1.141 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7% PEG 20K, 100mM sodium Citrate, 15% glycerol, 5mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→25 Å / Num. obs: 115113 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.07 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.043 / Rrim(I) all: 0.094 / Χ2: 1.629 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.882.20.50531230.0990.4220.6611.97697
1.88-1.922.20.58230800.4680.4880.7632.66397.6
1.92-1.952.30.42731500.0570.3550.5582.40897.8
1.95-1.992.40.30631460.5540.2380.3891.65398.4
1.99-2.042.50.23731830.8940.1770.2971.34199.2
2.04-2.082.70.31231800.8960.2240.3863.56298.9
2.08-2.142.90.21731840.4480.1530.2672.07599.6
2.14-2.193.10.19231600.940.1250.231.77799.9
2.19-2.263.50.23432060.3530.1480.2782.24999.9
2.26-2.333.80.19332250.8160.1120.2242.0799.9
2.33-2.414.20.14931630.9740.0820.1711.641100
2.41-2.514.70.13532250.9830.0690.1521.589100
2.51-2.625.50.12832080.9870.060.1421.604100
2.62-2.765.90.10731740.9880.0480.1181.487100
2.76-2.9460.08931860.9940.040.0981.367100
2.94-3.1660.07632120.9950.0340.0841.441100
3.16-3.4860.06731880.9960.030.0731.382100
3.48-3.985.90.0631950.9930.0270.0661.372100
3.98-5.015.90.05232170.9970.0240.0571.119100
5.01-255.60.05431830.9960.0250.0591.379100

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DFF

5dff


Resolution: 1.84→24.811 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.39
RfactorNum. reflection% reflection
Rfree0.2092 3621 3.15 %
Rwork0.1703 --
obs0.1715 115113 89.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.7 Å2 / Biso mean: 22.2407 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.84→24.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 849 17 564 5713
Biso mean--21.95 29.03 -
Num. residues----584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155398
X-RAY DIFFRACTIONf_angle_d1.4487502
X-RAY DIFFRACTIONf_chiral_restr0.082809
X-RAY DIFFRACTIONf_plane_restr0.009820
X-RAY DIFFRACTIONf_dihedral_angle_d19.1813079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86420.30921060.29293344345070
1.8642-1.88970.2831200.26983581370176
1.8897-1.91670.26771260.23983720384677
1.9167-1.94530.26391260.22253751387779
1.9453-1.97570.28491240.21863817394181
1.9757-2.00810.24651270.21364030415782
2.0081-2.04270.23051220.21033937405983
2.0427-2.07980.25091330.20964009414283
2.0798-2.11980.29741300.2044118424887
2.1198-2.1630.25061390.19394138427788
2.163-2.21010.28041390.19384299443889
2.2101-2.26140.23471360.1824228436490
2.2614-2.31790.2381470.1894464461191
2.3179-2.38060.25331380.18064332447093
2.3806-2.45060.26191440.1864531467594
2.4506-2.52960.25641490.17484499464895
2.5296-2.61990.22351500.1774664481496
2.6199-2.72470.2461490.1744562471196
2.7247-2.84850.20941500.17274659480997
2.8485-2.99840.21931500.18334649479997
2.9984-3.18590.19451490.17414668481798
3.1859-3.43130.16661540.15164683483798
3.4313-3.77560.18921540.14684677483198
3.7756-4.31940.17351500.1354703485398
4.3194-5.43260.15011550.12884718487399
5.4326-24.81280.1531540.14144711486598

+
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