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- PDB-5vez: DNA polymerase beta substrate complex with 8-oxoG:A at the primer... -

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Basic information

Entry
Database: PDB / ID: 5vez
TitleDNA polymerase beta substrate complex with 8-oxoG:A at the primer terminus and incoming dCTP analog
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
  • DNA (5'-D(P*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE/DNA / LIGASE/DNA / transferase ligase / DNA / TRANSFERASE-DNA / LIGASE-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 / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...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 / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / 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 / in utero embryonic development / microtubule / 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, thumb domain superfamily / DNA polymerase beta thumb / 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
Chem-XC5 / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.039 Å
AuthorsFreudenthal, B.D. / Schaich, M.A. / Whitaker, A.M. / Smith, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Capturing a mammalian DNA polymerase extending from an oxidized nucleotide.
Authors: Whitaker, A.M. / Smith, M.R. / Schaich, M.A. / Freudenthal, B.D.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 23, 2018Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_asym_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA (5'-D(*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')
D: DNA (5'-D(P*GP*TP*CP*GP*G)-3')
A: DNA polymerase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3069
Polymers47,7484
Non-polymers5585
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-62 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.469, 79.712, 55.523
Angle α, β, γ (deg.)90.00, 107.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(8OG))-3')


Mass: 3117.028 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#4: Protein DNA polymerase beta


Mass: 38241.672 Da / Num. of mol.: 1
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 , 4 types, 258 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-XC5 / 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine


Mass: 465.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O12P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.039→50 Å / Num. obs: 46175 / % possible obs: 99 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1263 / CC1/2: 0.817 / Rpim(I) all: 0.383 / Χ2: 1.111 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FMS

2fms


Resolution: 2.039→31.844 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2319 3497 7.57 %
Rwork0.1873 --
obs0.1907 46175 87.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.039→31.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 635 32 253 3524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073435
X-RAY DIFFRACTIONf_angle_d0.9414770
X-RAY DIFFRACTIONf_dihedral_angle_d18.0351986
X-RAY DIFFRACTIONf_chiral_restr0.049520
X-RAY DIFFRACTIONf_plane_restr0.005507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0389-2.06690.2709840.2825985X-RAY DIFFRACTION51
2.0669-2.09640.35361030.26961273X-RAY DIFFRACTION65
2.0964-2.12770.31991060.2641291X-RAY DIFFRACTION67
2.1277-2.16090.3041080.24921399X-RAY DIFFRACTION70
2.1609-2.19630.3531170.26131448X-RAY DIFFRACTION75
2.1963-2.23420.29981300.24611457X-RAY DIFFRACTION77
2.2342-2.27480.29871340.23651568X-RAY DIFFRACTION81
2.2748-2.31860.26681330.25071651X-RAY DIFFRACTION83
2.3186-2.36590.281310.2381676X-RAY DIFFRACTION88
2.3659-2.41730.29671570.22871891X-RAY DIFFRACTION94
2.4173-2.47350.26991460.22371809X-RAY DIFFRACTION96
2.4735-2.53530.27471570.22711888X-RAY DIFFRACTION95
2.5353-2.60390.29571500.22691830X-RAY DIFFRACTION96
2.6039-2.68040.2811620.22251881X-RAY DIFFRACTION96
2.6804-2.76690.29831460.2361833X-RAY DIFFRACTION95
2.7669-2.86570.31921490.22241836X-RAY DIFFRACTION95
2.8657-2.98040.24271540.22191868X-RAY DIFFRACTION96
2.9804-3.11590.2631490.21251877X-RAY DIFFRACTION96
3.1159-3.280.3411500.18711881X-RAY DIFFRACTION97
3.28-3.48530.18651570.17361920X-RAY DIFFRACTION97
3.4853-3.7540.18761520.14731857X-RAY DIFFRACTION97
3.754-4.13110.1631580.14151889X-RAY DIFFRACTION98
4.1311-4.72720.15281530.1371913X-RAY DIFFRACTION98
4.7272-5.94940.22141540.16251894X-RAY DIFFRACTION97
5.9494-31.84760.18041570.15881863X-RAY DIFFRACTION96

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