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- PDB-3oha: Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion -

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Basic information

Entry
Database: PDB / ID: 3oha
TitleYeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion
Components
  • 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'
  • 5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / Protein-DNA complex / Nucleotidyltransferase / DNA-directed DNA polymerase / DNA replication / DNA repair / DNA binding / nucleotide binding / metal binding / Nucleus / TRANSFERASE-DNA complex
Function / homology
Function and homology information


mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase ...mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / metal ion binding / nucleus
Similarity search - Function
DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain ...DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSilverstein, T.D. / Jain, R. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2010
Title: Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta.
Authors: Silverstein, T.D. / Jain, R. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / struct_site
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_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.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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,9609
Polymers66,1563
Non-polymers8046
Water12,701705
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-74 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.039, 227.635, 86.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / / Radiation-sensitive protein 30


Mass: 58813.402 Da / Num. of mol.: 1 / Fragment: UNP residues 1-513 / Mutation: K140A, S144W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DBH1, RAD30, YDR419W / Plasmid: pSL414 / Production host: Escherichia coli (E. coli) / Strain (production host): Er2566 / References: UniProt: Q04049, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'


Mass: 3205.100 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'


Mass: 4137.683 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 711 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% (w/v) polyethylene glycol 4000, 0.2 M lithium sulfate, 0.1 M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2008
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 58857 / % possible obs: 100 % / Redundancy: 6.1 % / Rsym value: 0.107 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2-2.0760.613100
2.07-2.156.10.461100
2.15-2.256.20.332100
2.25-2.376.20.271100
2.37-2.526.20.215100
2.52-2.716.20.156100
2.71-2.996.10.111100
2.99-3.426.10.076100
3.42-4.3160.05100
4.31-505.90.03299.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1JIH

1jih


Resolution: 2→34.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.296 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1278 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19511 2984 5.1 %RANDOM
Rwork0.15738 ---
obs0.15928 55839 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→34.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 490 45 705 5299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224886
X-RAY DIFFRACTIONr_bond_other_d0.0010.023131
X-RAY DIFFRACTIONr_angle_refined_deg1.5852.1016746
X-RAY DIFFRACTIONr_angle_other_deg0.95237716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0755551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32925.208192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1815772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5971518
X-RAY DIFFRACTIONr_chiral_restr0.090.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025131
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
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_it0.6781.52676
X-RAY DIFFRACTIONr_mcbond_other0.1931.51078
X-RAY DIFFRACTIONr_mcangle_it1.27224350
X-RAY DIFFRACTIONr_scbond_it2.01132210
X-RAY DIFFRACTIONr_scangle_it3.1074.52396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 181 -
Rwork0.219 3892 -
obs--94.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2575-1.0871-1.47482.35352.08673.03660.02420.03890.0296-0.0842-0.06-0.1139-0.0215-0.05260.03580.0372-0.0162-0.00620.06550.03710.0546-22.134543.70075.5543
20.8833-0.3414-0.33123.30621.58842.1125-0.06070.1364-0.194-0.19170.007-0.25730.23140.13750.05370.11330.02940.04950.10880.00820.1884-15.469924.8703-2.2085
31.0481-0.3638-0.24731.03590.67782.2105-0.0041-0.00760.02250.01170.021-0.1009-0.01870.158-0.01690.0048-0.0124-0.00350.04980.01880.0257-23.827355.240913.1531
44.7345-0.85430.3582.8583-0.21462.4970.0890.2499-0.4261-0.1449-0.08250.43220.1539-0.166-0.00650.03370.0069-0.01660.0746-0.02970.0878-47.983148.14040.2227
52.14390.86260.57772.31610.6683.56110.0480.0142-0.04520.0505-0.02130.20320.0475-0.1227-0.02670.16160.03730.04640.01850.02550.1745-31.603512.9744.1154
62.71460.6026-0.90573.177-0.22480.30430.0187-0.43510.2338-0.16860.0050.11720.01890.1504-0.02370.2595-0.04590.01030.24840.02010.2532-43.439424.53594.64
78.9641-0.2162-2.67040.46950.12450.81780.02020.23910.6868-0.15770.11040.27120.0083-0.1098-0.13060.2577-0.0409-0.01570.28720.0250.2749-40.404524.76532.5862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 72
2X-RAY DIFFRACTION2A73 - 150
3X-RAY DIFFRACTION3A151 - 306
4X-RAY DIFFRACTION4A307 - 388
5X-RAY DIFFRACTION5A389 - 512
6X-RAY DIFFRACTION6P1 - 11
7X-RAY DIFFRACTION7T4 - 16

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