[English] 日本語
Yorodumi
- PDB-7ef8: Crystal structure of mouse MUTYH in complex with DNA containing A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ef8
TitleCrystal structure of mouse MUTYH in complex with DNA containing AP site analogue:8-oxoG (Form I)
Components
  • Adenine DNA glycosylase
  • DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')
  • DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / negative regulation of necroptotic process / oxidized purine DNA binding ...adenine/guanine mispair binding / Displacement of DNA glycosylase by APEX1 / Cleavage of the damaged purine / adenine glycosylase / MutSalpha complex binding / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / purine-specific mismatch base pair DNA N-glycosylase activity / DNA N-glycosylase activity / negative regulation of necroptotic process / oxidized purine DNA binding / mismatch repair / base-excision repair / 4 iron, 4 sulfur cluster binding / response to oxidative stress / DNA repair / mitochondrion / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / 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 ...Endonuclease III, iron-sulphur binding site / Endonuclease III-like, conserved site-2 / Endonuclease III iron-sulfur binding region signature. / Endonuclease III family signature. / 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 domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Adenine DNA glycosylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsNakamura, T. / Nakabeppu, Y. / Yamagata, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structure of the mammalian adenine DNA glycosylase MUTYH: insights into the base excision repair pathway and cancer.
Authors: Nakamura, T. / Okabe, K. / Hirayama, S. / Chirifu, M. / Ikemizu, S. / Morioka, H. / Nakabeppu, Y. / Yamagata, Y.
History
DepositionMar 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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
A: Adenine DNA glycosylase
B: DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')
C: DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,76812
Polymers59,6793
Non-polymers1,0899
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-132 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.274, 107.236, 156.432
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Adenine DNA glycosylase / MutY homolog / mMYH


Mass: 51210.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mutyh, Myh / Production host: Escherichia coli (E. coli) / References: UniProt: Q99P21, adenine glycosylase

-
DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*TP*GP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*CP*T)-3')


Mass: 4385.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*GP*TP*CP*CP*CP*(3DR)P*GP*TP*CP*TP*C)-3')


Mass: 4082.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 75 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG3350, lithium sulfate, ammonium sulfate, Bis-Tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→46.89 Å / Num. obs: 23331 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 58.33 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 23.6
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.619 / Num. unique obs: 1142

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EF9

7ef9


Resolution: 2.45→46.89 Å / SU ML: 0.2966 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5168 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2206 1186 5.09 %
Rwork0.1976 22129 -
obs0.1988 23315 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.38 Å2
Refinement stepCycle: LAST / Resolution: 2.45→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 504 44 66 3786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293879
X-RAY DIFFRACTIONf_angle_d0.58495398
X-RAY DIFFRACTIONf_chiral_restr0.0362586
X-RAY DIFFRACTIONf_plane_restr0.0031607
X-RAY DIFFRACTIONf_dihedral_angle_d18.33171436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.560.35671500.27452671X-RAY DIFFRACTION97.82
2.56-2.70.27411520.25832710X-RAY DIFFRACTION99.93
2.7-2.870.26731320.25732769X-RAY DIFFRACTION99.86
2.87-3.090.28521510.262751X-RAY DIFFRACTION99.93
3.09-3.40.23421580.23222748X-RAY DIFFRACTION99.97
3.4-3.890.24451290.19562774X-RAY DIFFRACTION99.97
3.89-4.90.1851500.1652799X-RAY DIFFRACTION99.9
4.9-46.890.18591640.1692907X-RAY DIFFRACTION99.77
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)
12.67170131150.3119696499020.2374938270893.96031236924-1.029896057681.128623814590.188891669051-0.0499909724766-0.06865488352510.0788929473964-0.02794455857910.0535824177988-0.0341288541398-0.0120974514731-0.1319502872730.418800066037-0.007994038703430.05636416775740.37265316677-0.03770768671730.31381992504976.823609646115.699113675831.2387521161
22.496679052281.212329089990.5495178400674.17849397273-0.003974472124773.373500233540.02386282685440.777526086164-0.178381381378-0.712618558476-0.00143823781694-1.033449681710.1066942361650.776636528432-0.01518497795650.5476758361790.07912408127010.23728552310.728615438663-0.02341855152440.738879490866102.93345789616.699273323420.6176652421
33.109382575580.273171517653-1.425851747512.52487668605-0.06249488831646.62060283650.1071767277230.2526229336890.184211716251-0.2265564342030.1329729975960.360735545901-0.537290245084-0.416702958669-0.2153552869290.5656855507740.08615281967050.03857352640010.3925089742390.08738626085160.4975156220663.35780226440.791368210916.8255039745
47.497481429280.3940264714070.848219809575.66609459202-1.053127964416.284687496170.2811985682230.7076393542010.208004089435-0.9536863614210.0724062680179-1.332487127710.3109101757270.87277208317-0.4251684714290.695227301241-0.01074640873290.2270776892950.640168536971-0.01066845378780.60498001683984.673273780527.383262436515.1038865841
57.202822854113.30446473506-0.8043989077412.40626706535-0.8590342334464.631439540250.0002032408344350.4381127367321.74982073024-1.88089676434-0.227547513720.759287352502-0.5802743655120.1213608071750.3076593451350.9479783069370.05940896721190.1050602026550.6261654513320.01810333081860.96445713005386.581803999528.482202952615.9056099347
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 86:200 )
2X-RAY DIFFRACTION2chain 'A' and ((resid 52:79) or (resid 201:331))
3X-RAY DIFFRACTION3chain 'A' and (resid 332:470)
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 13 )

+
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