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- PDB-6uok: Y271G DNA polymerase beta substrate complex with templating cytos... -

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Basic information

Entry
Database: PDB / ID: 6uok
TitleY271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / DNA Polymerase / oxidized ribonucleotide / DNA damage / DNA BINDING PROTEIN / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair, gap-filling / response to gamma radiation / base-excision repair / spindle microtubule / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / microtubule / in utero embryonic development / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family ...DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
8-OXO-GUANOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSmith, M.R. / Freudenthal, B.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase beta.
Authors: Smith, M.R. / Alnajjar, K.S. / Hoitsma, N.M. / Sweasy, J.B. / Freudenthal, B.D.
History
DepositionOct 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
E: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
F: DNA polymerase beta
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,75925
Polymers95,0918
Non-polymers1,66817
Water84747
1
B: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
C: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
E: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
F: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,46414
Polymers47,5464
Non-polymers91810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-89 kcal/mol
Surface area19720 Å2
MethodPISA
2
A: DNA polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,29511
Polymers47,5464
Non-polymers7497
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-65 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.687, 79.957, 100.832
Angle α, β, γ (deg.)90.000, 97.642, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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DNA chain , 3 types, 6 molecules BTCPED

#1: DNA chain DNA (5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')


Mass: 4829.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3')


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules FA

#4: Protein DNA polymerase beta


Mass: 38135.551 Da / Num. of mol.: 2 / Mutation: Y271G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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Non-polymers , 7 types, 64 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-8GT / 8-OXO-GUANOSINE-5'-TRIPHOSPHATE


Mass: 539.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O15P3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 19% PEG3350, 0.05M Imidazole (pH 8.0), 0.35 Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.55→25 Å / Num. obs: 42693 / % possible obs: 99.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 40.22 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.062 / Rrim(I) all: 0.124 / Χ2: 0.976 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Χ2% possible allRpim(I) allRmerge(I) obsRrim(I) all
2.55-2.593.914300.3850.90199.7
2.59-2.644.314090.4320.928100
2.64-2.694.614170.5910.93699.90.741
2.69-2.754.714370.6910.8711000.56
2.75-2.814.713910.7140.90699.90.549
2.81-2.874.814230.7720.91799.90.4480.8820.993
2.87-2.944.914020.8180.93499.90.3550.7060.794
2.94-3.02514310.8550.94699.80.2890.5790.649
3.02-3.11513900.9040.9799.90.2150.4330.485
3.11-3.215.114440.9520.9781000.1260.2550.285
3.21-3.335.114090.9830.93999.90.0750.1540.172
3.33-3.465.114460.9840.92299.90.0560.1160.129
3.46-3.625.114070.9840.92699.90.050.1030.115
3.62-3.815.114160.9871.0281000.0480.0990.111
3.81-4.04514470.9880.9321000.0420.0880.098
4.04-4.35514090.9870.9351000.0380.0780.087
4.35-4.79514350.9860.9521000.0380.080.089
4.79-5.484.914370.9841.0681000.0390.0810.09
5.48-6.884.814530.9831.14799.90.0380.0790.088
6.88-254.414760.9941.38799.90.0310.0620.069

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data collection
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 2.55→24.14 Å / SU ML: 0.3815 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7583
RfactorNum. reflection% reflection
Rfree0.2787 3344 7.83 %
Rwork0.2243 --
obs0.2285 42693 76.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.09 Å2
Refinement stepCycle: LAST / Resolution: 2.55→24.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 1255 84 47 6453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416660
X-RAY DIFFRACTIONf_angle_d0.61629253
X-RAY DIFFRACTIONf_chiral_restr0.04821019
X-RAY DIFFRACTIONf_plane_restr0.0032968
X-RAY DIFFRACTIONf_dihedral_angle_d26.08312546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.570.2973420.342514X-RAY DIFFRACTION23.46
2.57-2.610.4573610.3191704X-RAY DIFFRACTION32.96
2.61-2.650.3317640.3167777X-RAY DIFFRACTION36.98
2.65-2.690.3831770.3271953X-RAY DIFFRACTION43.76
2.69-2.740.34960.33591059X-RAY DIFFRACTION48.12
2.74-2.790.3881930.33441081X-RAY DIFFRACTION52.2
2.79-2.840.53141080.38711268X-RAY DIFFRACTION57.69
2.84-2.90.42311160.36821354X-RAY DIFFRACTION63.53
2.9-2.970.50091250.37881499X-RAY DIFFRACTION69.28
2.97-3.030.42191350.34391637X-RAY DIFFRACTION75.69
3.03-3.110.40931540.29721699X-RAY DIFFRACTION80.25
3.11-3.190.3361630.28571897X-RAY DIFFRACTION86.08
3.19-3.290.29031640.27151965X-RAY DIFFRACTION92.61
3.29-3.390.26221770.22482074X-RAY DIFFRACTION96.86
3.39-3.510.30121800.21322088X-RAY DIFFRACTION97.89
3.51-3.660.24071740.20462139X-RAY DIFFRACTION98.05
3.66-3.820.29951780.20642087X-RAY DIFFRACTION97.59
3.82-4.020.29161790.19462147X-RAY DIFFRACTION97.98
4.02-4.270.25021770.18092054X-RAY DIFFRACTION97.47
4.27-4.60.21041780.18882132X-RAY DIFFRACTION97.55
4.6-5.060.24351800.17982078X-RAY DIFFRACTION97.16
5.06-5.780.19771800.19212057X-RAY DIFFRACTION96.3
5.78-7.250.23771670.20652065X-RAY DIFFRACTION95.22
7.25-24.140.20721760.17612021X-RAY DIFFRACTION93.89

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