[English] 日本語
Yorodumi
- PDB-7ayy: Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ayy
TitleStructure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / 8-oxoguanine DNA glycosylase / N-glycosylase / DNA lyase / DNA repair
Function / homology
Function and homology information


Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 ...Defective OGG1 Substrate Binding / Defective OGG1 Substrate Processing / Defective OGG1 Localization / depurination / negative regulation of double-strand break repair via single-strand annealing / oxidized purine nucleobase lesion DNA N-glycosylase activity / base-excision repair, AP site formation / depyrimidination / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / positive regulation of gene expression via chromosomal CpG island demethylation / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to reactive oxygen species / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / response to oxidative stress / endonuclease activity / microtubule binding / damaged DNA binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / mitochondrial matrix / DNA damage response / regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / DNA glycosylase
Similarity search - Domain/homology
~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMasuyer, G. / Davies, J.R. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Science / Year: 2022
Title: Small-molecule activation of OGG1 increases oxidative DNA damage repair by gaining a new function.
Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / ...Authors: Michel, M. / Benitez-Buelga, C. / Calvo, P.A. / Hanna, B.M.F. / Mortusewicz, O. / Masuyer, G. / Davies, J. / Wallner, O. / Sanjiv, K. / Albers, J.J. / Castaneda-Zegarra, S. / Jemth, A.S. / Visnes, T. / Sastre-Perona, A. / Danda, A.N. / Homan, E.J. / Marimuthu, K. / Zhenjun, Z. / Chi, C.N. / Sarno, A. / Wiita, E. / von Nicolai, C. / Komor, A.J. / Rajagopal, V. / Muller, S. / Hank, E.C. / Varga, M. / Scaletti, E.R. / Pandey, M. / Karsten, S. / Haslene-Hox, H. / Loevenich, S. / Marttila, P. / Rasti, A. / Mamonov, K. / Ortis, F. / Schomberg, F. / Loseva, O. / Stewart, J. / D'Arcy-Evans, N. / Koolmeister, T. / Henriksson, M. / Michel, D. / de Ory, A. / Acero, L. / Calvete, O. / Scobie, M. / Hertweck, C. / Vilotijevic, I. / Kalderen, C. / Osorio, A. / Perona, R. / Stolz, A. / Stenmark, P. / Berglund, U.W. / de Vega, M. / Helleday, T.
History
DepositionNov 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.2Jan 31, 2024Group: 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
AAA: N-glycosylase/DNA lyase
BBB: N-glycosylase/DNA lyase
CCC: N-glycosylase/DNA lyase
DDD: N-glycosylase/DNA lyase
EEE: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,71615
Polymers189,6095
Non-polymers2,10710
Water12,683704
1
AAA: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3843
Polymers37,9221
Non-polymers4632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3843
Polymers37,9221
Non-polymers4632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1892
Polymers37,9221
Non-polymers2671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2813
Polymers37,9221
Non-polymers3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4774
Polymers37,9221
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.025, 86.025, 427.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
N-glycosylase/DNA lyase


Mass: 37921.879 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Truncated version of hOGG1 / Source: (gene. exp.) Homo sapiens (human) / Gene: OGG1, MMH, MUTM, OGH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O15527, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical
ChemComp-SEQ / ~{N}-cyclohexyl-2-cyclopropyl-quinazolin-4-amine / TH10785


Mass: 267.369 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H21N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5 and 48 % v/v Precipitant Mix 4 (Morpheus screen, Molecular Dimensions)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2→86.03 Å / Num. obs: 110134 / % possible obs: 100 % / Redundancy: 24.1 % / Biso Wilson estimate: 22.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.299 / Rpim(I) all: 0.087 / Rrim(I) all: 0.311 / Net I/σ(I): 8.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 19 % / Rmerge(I) obs: 2.65 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5306 / CC1/2: 0.529 / Rpim(I) all: 0.886 / Rrim(I) all: 2.79 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RLW

6rlw


Resolution: 2→84.478 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.496 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.21 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2503 5445 4.962 %
Rwork0.207 104291 -
all0.209 --
obs-109736 99.799 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.456 Å20 Å20 Å2
2---0.456 Å20 Å2
3---0.911 Å2
Refinement stepCycle: LAST / Resolution: 2→84.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12158 0 148 704 13010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312650
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711463
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.64717201
X-RAY DIFFRACTIONr_angle_other_deg1.2791.58126543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87151514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58321.067703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.05415105
X-RAY DIFFRACTIONr_chiral_restr0.0680.21555
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022849
X-RAY DIFFRACTIONr_nbd_refined0.1980.22562
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.210545
X-RAY DIFFRACTIONr_nbtor_refined0.1630.26082
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25358
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2693
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.245
X-RAY DIFFRACTIONr_nbd_other0.2230.2142
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0730.21
X-RAY DIFFRACTIONr_mcbond_it1.9752.7786101
X-RAY DIFFRACTIONr_mcbond_other1.9752.7776100
X-RAY DIFFRACTIONr_mcangle_it3.124.1477600
X-RAY DIFFRACTIONr_mcangle_other3.124.1487601
X-RAY DIFFRACTIONr_scbond_it2.5923.1666548
X-RAY DIFFRACTIONr_scbond_other2.5923.1676549
X-RAY DIFFRACTIONr_scangle_it4.2094.6299586
X-RAY DIFFRACTIONr_scangle_other4.2094.639587
X-RAY DIFFRACTIONr_lrange_it6.02332.85814523
X-RAY DIFFRACTIONr_lrange_other5.99532.73814394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.323810.3127578X-RAY DIFFRACTION99.9247
2.052-2.1080.3363740.2997387X-RAY DIFFRACTION99.7045
2.108-2.1690.3053920.2657152X-RAY DIFFRACTION99.7092
2.169-2.2360.2993610.2566992X-RAY DIFFRACTION99.7423
2.236-2.3090.2993410.2416790X-RAY DIFFRACTION99.7064
2.309-2.390.2563400.2186637X-RAY DIFFRACTION99.7569
2.39-2.480.2923280.2246314X-RAY DIFFRACTION99.7148
2.48-2.5820.2763210.2096125X-RAY DIFFRACTION99.8606
2.582-2.6960.2523200.2075909X-RAY DIFFRACTION99.7917
2.696-2.8280.2863050.2115625X-RAY DIFFRACTION99.8653
2.828-2.9810.2342910.1965374X-RAY DIFFRACTION99.859
2.981-3.1610.2322780.1925096X-RAY DIFFRACTION99.8885
3.161-3.380.2562430.1984833X-RAY DIFFRACTION99.9016
3.38-3.650.252140.1914506X-RAY DIFFRACTION99.8519
3.65-3.9980.1892180.164178X-RAY DIFFRACTION99.9091
3.998-4.4690.1931970.1513815X-RAY DIFFRACTION99.8507
4.469-5.1590.1872140.1653340X-RAY DIFFRACTION99.8315
5.159-6.3150.2471280.2152936X-RAY DIFFRACTION99.7721
6.315-8.9150.2491190.1742314X-RAY DIFFRACTION99.8768

+
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