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- PDB-6g3y: Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in comp... -

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Basic information

Entry
Database: PDB / ID: 6g3y
TitleStructure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH5675
ComponentsN-glycosylase/DNA lyase
KeywordsDNA BINDING PROTEIN / N-glycosylase / DNA lyase
Function / homology
Function and homology information


Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / 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 / 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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity ...Cleavage of the damaged pyrimidine / oxidized base lesion DNA N-glycosylase activity / Displacement of DNA glycosylase by APEX1 / 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 / 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 / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / DNA N-glycosylase activity / positive regulation of gene expression via chromosomal CpG island demethylation / response to folic acid / oxidized purine DNA binding / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / response to light stimulus / cellular response to cadmium ion / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / response to radiation / nuclear matrix / cellular response to reactive oxygen species / response to estradiol / microtubule binding / response to ethanol / response to oxidative stress / damaged DNA binding / nuclear speck / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA repair / 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 / mitochondrion / DNA binding / nucleoplasm / nucleus
Similarity search - Function
TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal ...TATA-Binding Protein - #40 / 8-oxoguanine DNA-glycosylase / 8-oxoguanine DNA glycosylase, N-terminal / : / 8-oxoguanine DNA glycosylase, N-terminal domain / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / TATA-Binding Protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-ELB / NICKEL (II) ION / N-glycosylase/DNA lyase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMasuyer, G. / Helleday, T. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Science / Year: 2018
Title: Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.
Authors: Visnes, T. / Cazares-Korner, A. / Hao, W. / Wallner, O. / Masuyer, G. / Loseva, O. / Mortusewicz, O. / Wiita, E. / Sarno, A. / Manoilov, A. / Astorga-Wells, J. / Jemth, A.S. / Pan, L. / ...Authors: Visnes, T. / Cazares-Korner, A. / Hao, W. / Wallner, O. / Masuyer, G. / Loseva, O. / Mortusewicz, O. / Wiita, E. / Sarno, A. / Manoilov, A. / Astorga-Wells, J. / Jemth, A.S. / Pan, L. / Sanjiv, K. / Karsten, S. / Gokturk, C. / Grube, M. / Homan, E.J. / Hanna, B.M.F. / Paulin, C.B.J. / Pham, T. / Rasti, A. / Berglund, U.W. / von Nicolai, C. / Benitez-Buelga, C. / Koolmeister, T. / Ivanic, D. / Iliev, P. / Scobie, M. / Krokan, H.E. / Baranczewski, P. / Artursson, P. / Altun, M. / Jensen, A.J. / Kalderen, C. / Ba, X. / Zubarev, R.A. / Stenmark, P. / Boldogh, I. / Helleday, T.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn ...pdbx_data_processing_status / struct_conn / struct_conn_type / struct_site / struct_site_gen
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-glycosylase/DNA lyase
B: N-glycosylase/DNA lyase
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0008
Polymers107,4503
Non-polymers1,5505
Water2,198122
1
A: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3533
Polymers35,8171
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3533
Polymers35,8171
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-glycosylase/DNA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2942
Polymers35,8171
Non-polymers4771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.817, 81.357, 169.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein N-glycosylase/DNA lyase


Mass: 35816.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Recombinant construct of mouse OGG1 residues 11-325. Expressed with a cleavable N-terminal his tag (residues 8-10 from expression tag after cleavage)
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ogg1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O08760, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-ELB / 4-(4-azanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide / TH5675


Mass: 477.299 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H20IN5O2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.09 M Halogens, 0.1 M Buffer System 2 pH 7.5, 50 % v/v Precipitant Mix 3 (Morpheus screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.51→84.58 Å / Num. obs: 38585 / % possible obs: 99.6 % / Redundancy: 7 % / CC1/2: 0.976 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.126 / Net I/σ(I): 9.3
Reflection shellResolution: 2.51→2.56 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1719 / CC1/2: 0.137 / Rpim(I) all: 0.338 / Rrim(I) all: 0.918 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EBM

1ebm


Resolution: 2.51→84.58 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 14.199 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.702 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28215 1862 4.8 %RANDOM
Rwork0.23416 ---
obs0.23635 36660 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.336 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.92 Å2
Refinement stepCycle: 1 / Resolution: 2.51→84.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7531 0 86 122 7739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197848
X-RAY DIFFRACTIONr_bond_other_d0.0010.027078
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.9510687
X-RAY DIFFRACTIONr_angle_other_deg0.893316376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135945
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07422.992371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.496151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1451564
X-RAY DIFFRACTIONr_chiral_restr0.0580.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021717
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6347.4883790
X-RAY DIFFRACTIONr_mcbond_other2.6337.4883788
X-RAY DIFFRACTIONr_mcangle_it4.5811.2244731
X-RAY DIFFRACTIONr_mcangle_other4.5811.2244732
X-RAY DIFFRACTIONr_scbond_it2.0327.5254058
X-RAY DIFFRACTIONr_scbond_other2.0317.5254059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.57811.2055957
X-RAY DIFFRACTIONr_long_range_B_refined6.85983.9458743
X-RAY DIFFRACTIONr_long_range_B_other6.85983.9488739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.514→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 135 -
Rwork0.352 2478 -
obs--92.99 %

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