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- PDB-4o3s: Crystal structure of human polymerase eta extending an 8-oxog dna... -

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Basic information

Entry
Database: PDB / ID: 4o3s
TitleCrystal structure of human polymerase eta extending an 8-oxog dna lesion: post insertion of 8-oxog-dc pair
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*C)-3')
  • DNA (5'-D(*CP*AP*TP*GP*(8OG)P*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTransferase/DNA / Catalytic Domain / DNA / DNA Damage / DNA-Directed DNA Polymerase / Cytosine Triphosphate / Y-family polymerase / trans-lesion synthesis (TLS) / DNA Binding / 8-oxoG lesion bypass / Transferase-DNA complex
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / 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 / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / 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 / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / 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
Chem-0KX / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.717 Å
AuthorsPatra, A. / Egli, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Human DNA Polymerase eta
Authors: Patra, A. / Nagy, L.D. / Zhang, Q. / Su, Y. / Muller, L. / Guengerich, F.P. / Egli, M.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Sep 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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
T: DNA (5'-D(*CP*AP*TP*GP*(8OG)P*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0387
Polymers54,4313
Non-polymers6074
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-41 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.312, 98.312, 81.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48325.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*CP*AP*TP*GP*(8OG)P*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3694.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*C)-3')


Mass: 2411.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically Synthesized

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Non-polymers , 4 types, 456 molecules

#4: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES pH 5.5, 5mM magnesium chloride, 17% PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 21, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 47707 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 31.255
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.72-1.756.60.7572.62223890.75799.2
1.75-1.786.60.6353.19423400.63599.5
1.78-1.826.70.5563.66723690.55699.3
1.82-1.856.70.484.36123930.4899.9
1.85-1.896.80.3895.38923630.38999.6
1.89-1.946.80.3246.44423800.32499.6
1.94-1.9970.2618.22223580.26199.5
1.99-2.047.10.2181023630.21899.7
2.04-2.17.20.17812.32424100.17899.7
2.1-2.177.40.14715.16723800.14799.9
2.17-2.247.50.12317.97323950.12399.9

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBLdata collection
PHASER(MR)phasing
PHENIX(phenix.refine: dev_1551)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ECQ

4ecq


Resolution: 1.717→42.57 Å / SU ML: 0.19 / Isotropic thermal model: Isotropic / σ(F): 1.35 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 2412 5.06 %RANDOM
Rwork0.1723 ---
obs0.1742 47707 99.71 %-
all-47847 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.717→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 390 36 452 4223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073935
X-RAY DIFFRACTIONf_angle_d1.1635412
X-RAY DIFFRACTIONf_dihedral_angle_d19.6791536
X-RAY DIFFRACTIONf_chiral_restr0.046606
X-RAY DIFFRACTIONf_plane_restr0.005625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7169-1.7520.29881300.23182629X-RAY DIFFRACTION99
1.752-1.79010.26031440.22262648X-RAY DIFFRACTION99
1.7901-1.83170.29051550.2062652X-RAY DIFFRACTION100
1.8317-1.87750.25361440.19242619X-RAY DIFFRACTION100
1.8775-1.92830.25691520.18872656X-RAY DIFFRACTION100
1.9283-1.9850.21711300.18642665X-RAY DIFFRACTION100
1.985-2.04910.27851390.18482672X-RAY DIFFRACTION100
2.0491-2.12240.23291200.17792655X-RAY DIFFRACTION100
2.1224-2.20730.20721560.17632649X-RAY DIFFRACTION100
2.2073-2.30780.19291360.16622660X-RAY DIFFRACTION100
2.3078-2.42940.22141390.16982677X-RAY DIFFRACTION100
2.4294-2.58160.20991360.18212679X-RAY DIFFRACTION100
2.5816-2.78090.22371540.17532670X-RAY DIFFRACTION100
2.7809-3.06070.1981290.17642689X-RAY DIFFRACTION100
3.0607-3.50340.19031400.15762687X-RAY DIFFRACTION100
3.5034-4.41320.1811500.14292687X-RAY DIFFRACTION100
4.4132-42.58340.19971580.17722701X-RAY DIFFRACTION99

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