[English] 日本語
Yorodumi
- PDB-8dvp: Glycosylase MutY variant N146S in complex with DNA containing d(8... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dvp
TitleGlycosylase MutY variant N146S in complex with DNA containing d(8-oxo-G) paired with substrate purine
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3')
KeywordsHYDROLASE/DNA / Protein-DNA complex / DNA repair / Base Excision Repair / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / adenine glycosylase / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / DNA binding / metal ion binding
Similarity search - Function
A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein ...A/G-specific adenine glycosylase MutY / Iron-sulfur binding domain of endonuclease III / Adenine/Thymine-DNA glycosylase / MutY, C-terminal / NUDIX domain / Helix-hairpin-helix motif / Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-helix motif / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsDemir, M. / Russelburg, L.P. / Horvath, M.P. / David, S.S.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1905304 United States
National Science Foundation (NSF, United States)1905249 United States
National Science Foundation (NSF, United States)1610721 United States
National Science Foundation (NSF, United States)1608934 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism.
Authors: Demir, M. / Russelburg, L.P. / Lin, W.J. / Trasvina-Arenas, C.H. / Huang, B. / Yuen, P.K. / Horvath, M.P. / David, S.S.
History
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
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 / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenine DNA glycosylase
B: DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0108
Polymers48,4793
Non-polymers5315
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-72 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.680, 86.170, 140.770
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

-
Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / oxoG:A-specific adenine glycosylase


Mass: 41746.574 Da / Num. of mol.: 1 / Mutation: N146S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83847

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')


Mass: 3423.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3')


Mass: 3309.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 185 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, calcium acetate, ethylene glycol, Tris.HCl, b-mercaptoethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11585 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 6, 2019
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11585 Å / Relative weight: 1
ReflectionResolution: 1.54→73.49 Å / Num. obs: 130827 / % possible obs: 99.8 % / Redundancy: 12.8 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.15
Reflection shellResolution: 1.54→1.58 Å / Num. unique obs: 9558 / CC1/2: 0.146 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U7T

6u7t


Resolution: 1.54→73.49 Å / SU ML: 0.2817 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.283
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 3269 2.51 %
Rwork0.2172 127010 -
obs0.2176 130279 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.58 Å2
Refinement stepCycle: LAST / Resolution: 1.54→73.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 431 15 180 3308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01363279
X-RAY DIFFRACTIONf_angle_d1.29064582
X-RAY DIFFRACTIONf_chiral_restr0.0763515
X-RAY DIFFRACTIONf_plane_restr0.0124512
X-RAY DIFFRACTIONf_dihedral_angle_d17.60611200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.42821330.39965057X-RAY DIFFRACTION89.81
1.56-1.590.41051330.36195383X-RAY DIFFRACTION98.13
1.59-1.610.34651450.34745562X-RAY DIFFRACTION99.86
1.61-1.640.31891420.32965545X-RAY DIFFRACTION100
1.64-1.670.29751390.31745511X-RAY DIFFRACTION99.96
1.67-1.70.34081500.31735620X-RAY DIFFRACTION100
1.7-1.740.3331370.32155521X-RAY DIFFRACTION99.93
1.74-1.780.31781480.31295559X-RAY DIFFRACTION99.88
1.78-1.820.33781400.29825571X-RAY DIFFRACTION99.98
1.82-1.860.24421500.29135504X-RAY DIFFRACTION99.95
1.86-1.910.32061480.28375562X-RAY DIFFRACTION99.98
1.91-1.970.30931360.2665599X-RAY DIFFRACTION99.95
1.97-2.030.29111390.26395508X-RAY DIFFRACTION100
2.03-2.110.31381470.2635602X-RAY DIFFRACTION99.98
2.11-2.190.24531430.26695520X-RAY DIFFRACTION100
2.19-2.290.25791580.24345534X-RAY DIFFRACTION99.96
2.29-2.410.21611500.22725552X-RAY DIFFRACTION100
2.41-2.560.22331450.23625545X-RAY DIFFRACTION99.98
2.56-2.760.20491450.22895535X-RAY DIFFRACTION99.84
2.76-3.040.23561380.22725559X-RAY DIFFRACTION99.88
3.04-3.480.23521380.18825566X-RAY DIFFRACTION99.81
3.48-4.380.19071240.16525531X-RAY DIFFRACTION99.58
4.38-73.490.18541410.17385564X-RAY DIFFRACTION99.83
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)
12.99651754112-0.417442019333-0.2616586485021.1501475325-0.037050756270.2940733734890.1758889176310.7804234948660.0222123894768-0.136448760428-0.135015975719-0.0120057609938-0.04597568864980.00917834664917-0.004497106821150.2213587031570.05710047587110.000797184426210.3186751832310.0007045811029760.19169188654212.84263489412.166997224162.92969329919
20.152380230872-0.07468340583010.01079602825270.2909346954480.1191452732790.3349657207150.0038638437325-0.3844787280360.1800435723790.1790612210570.135414520026-0.161514068112-0.009036509921080.3226001029260.0002800952978850.402045287213-0.00297593831486-0.0421512735460.50949701655-0.09346192698580.28455635893220.90381268947.6458334909837.6305707475
30.371643277986-0.327314820916-0.07984302237930.571293947366-0.03848342577010.0989666612366-0.00329099477321-0.179066282893-0.234437308874-0.18535297174-0.0774174213484-0.02367046222590.3078517695230.234026587925-2.04522619799E-50.3243328276090.00868092125612-0.004295111894520.2753970268290.03592559371640.31450834179519.9079299139-3.8564099968115.8811501912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and (resid 7:228 or resid 401 or resid 403))AA - G7 - 4031
22(chain A and (resid 229:360 or resid 404))AA - H229 - 404223
33((chain B and resid 1:11) or (chain C and (resid 12:22 or resid 101)))B - CD - F1 - 101

+
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