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- PDB-6rlw: Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 6rlw
TitleStructure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with inhibitor TH5487
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / DNA repair / cancer / small molecule inhibitor
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 / positive regulation of gene expression via chromosomal CpG island demethylation / 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 / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / response to light stimulus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / response to radiation / base-excision repair / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / endonuclease activity / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / mitochondrial matrix / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / 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
Chem-K8Q / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMasuyer, G. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Targeting OGG1 arrests cancer cell proliferation by inducing replication stress.
Authors: Visnes, T. / Benitez-Buelga, C. / Cazares-Korner, A. / Sanjiv, K. / Hanna, B.M.F. / Mortusewicz, O. / Rajagopal, V. / Albers, J.J. / Hagey, D.W. / Bekkhus, T. / Eshtad, S. / Baquero, J.M. / ...Authors: Visnes, T. / Benitez-Buelga, C. / Cazares-Korner, A. / Sanjiv, K. / Hanna, B.M.F. / Mortusewicz, O. / Rajagopal, V. / Albers, J.J. / Hagey, D.W. / Bekkhus, T. / Eshtad, S. / Baquero, J.M. / Masuyer, G. / Wallner, O. / Muller, S. / Pham, T. / Gokturk, C. / Rasti, A. / Suman, S. / Torres-Ruiz, R. / Sarno, A. / Wiita, E. / Homan, E.J. / Karsten, S. / Marimuthu, K. / Michel, M. / Koolmeister, T. / Scobie, M. / Loseva, O. / Almlof, I. / Unterlass, J.E. / Pettke, A. / Bostrom, J. / Pandey, M. / Gad, H. / Herr, P. / Jemth, A.S. / El Andaloussi, S. / Kalderen, C. / Rodriguez-Perales, S. / Benitez, J. / Krokan, H.E. / Altun, M. / Stenmark, P. / Berglund, U.W. / Helleday, T.
History
DepositionMay 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)192,31510
Polymers189,6095
Non-polymers2,7065
Water13,890771
1
AAA: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers37,9221
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers37,9221
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers37,9221
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers37,9221
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
EEE: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4632
Polymers37,9221
Non-polymers5411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.367, 86.367, 432.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
N-glycosylase/DNA lyase


Mass: 37921.879 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: His-tagged recombinant human OGG1[11-327] / 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-K8Q / 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide


Mass: 541.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H18BrIN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 48 % v/v Precipitant Mix from 4 Morpheus screen (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→86.4 Å / Num. obs: 112319 / % possible obs: 100 % / Redundancy: 21.8 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1 / Χ2: 1.01 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 20.6 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5469 / CC1/2: 0.846 / Rpim(I) all: 0.39 / Rrim(I) all: 1.28 / Χ2: 1.06 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBM

1ebm


Resolution: 2→84.837 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.611 / SU ML: 0.152 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2741 5560 4.967 %
Rwork0.2225 --
all0.225 --
obs-111929 99.859 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.301 Å2
Baniso -1Baniso -2Baniso -3
1--0.888 Å20 Å20 Å2
2---0.888 Å20 Å2
3---1.777 Å2
Refinement stepCycle: LAST / Resolution: 2→84.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12267 0 135 771 13173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01312764
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711500
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.63417368
X-RAY DIFFRACTIONr_angle_other_deg1.2051.57926620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7451533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.93821.141710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.025152015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.76715105
X-RAY DIFFRACTIONr_chiral_restr0.0590.21565
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022885
X-RAY DIFFRACTIONr_nbd_refined0.1880.22561
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.210736
X-RAY DIFFRACTIONr_nbtor_refined0.1590.26084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25366
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2730
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.239
X-RAY DIFFRACTIONr_nbd_other0.1750.2125
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.228
X-RAY DIFFRACTIONr_mcbond_it2.4494.2626165
X-RAY DIFFRACTIONr_mcbond_other2.4494.2626166
X-RAY DIFFRACTIONr_mcangle_it3.7926.3767697
X-RAY DIFFRACTIONr_mcangle_other3.796.3767696
X-RAY DIFFRACTIONr_scbond_it2.5954.6486599
X-RAY DIFFRACTIONr_scbond_other2.5844.6486598
X-RAY DIFFRACTIONr_scangle_it4.1216.8559671
X-RAY DIFFRACTIONr_scangle_other4.1216.8569672
X-RAY DIFFRACTIONr_lrange_it6.34450.06414475
X-RAY DIFFRACTIONr_lrange_other6.3450.03214447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.3323790.2887769X-RAY DIFFRACTION99.9877
2.052-2.1080.3274180.2777550X-RAY DIFFRACTION99.9874
2.108-2.1690.3313490.2577351X-RAY DIFFRACTION99.9611
2.169-2.2360.3493350.2677134X-RAY DIFFRACTION99.8796
2.236-2.3090.3243720.2786934X-RAY DIFFRACTION99.836
2.309-2.390.2913700.2356709X-RAY DIFFRACTION99.9576
2.39-2.480.2973450.2356484X-RAY DIFFRACTION99.9561
2.48-2.5820.263330.226226X-RAY DIFFRACTION99.9848
2.582-2.6960.3022830.2346061X-RAY DIFFRACTION99.9685
2.696-2.8280.2983250.2365720X-RAY DIFFRACTION99.9504
2.828-2.9810.2792910.2245526X-RAY DIFFRACTION99.8798
2.981-3.1610.2762770.235157X-RAY DIFFRACTION99.9081
3.161-3.380.2722570.2164924X-RAY DIFFRACTION99.7881
3.38-3.650.2292520.2174574X-RAY DIFFRACTION99.6901
3.65-3.9980.2642050.1974246X-RAY DIFFRACTION99.6418
3.998-4.4690.2542330.183840X-RAY DIFFRACTION99.7307
4.469-5.1590.2451550.1833478X-RAY DIFFRACTION99.6161
5.159-6.3150.311650.2342922X-RAY DIFFRACTION99.2924
6.315-8.9150.2511390.2152345X-RAY DIFFRACTION99.639

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