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- PDB-4j9r: Human DNA polymerase eta-DNA translocated binary complex with TG ... -

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Basic information

Entry
Database: PDB / ID: 4j9r
TitleHuman DNA polymerase eta-DNA translocated binary complex with TG mispair
Components
  • DNA (5'-D(*T*AP*CP*TP*TP*AP*TP*GP*AP*CP*GP*T)-3')
  • DNA (5'-D(P*TP*AP*CP*GP*TP*CP*AP*TP*G)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / immunoglobulin / A to G transition / misincorporation / wobble base pair / DNA polymerase / 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
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsZhao, Y. / Gregory, M. / Biertumpfel, C. / Hua, Y. / Hanaoka, F. / Yang, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Mechanism of somatic hypermutation at the WA motif by human DNA polymerase eta.
Authors: Zhao, Y. / Gregory, M.T. / Biertumpfel, C. / Hua, Y.J. / Hanaoka, F. / Yang, W.
History
DepositionFeb 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: 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 / 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 / _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
T: DNA (5'-D(*T*AP*CP*TP*TP*AP*TP*GP*AP*CP*GP*T)-3')
P: DNA (5'-D(P*TP*AP*CP*GP*TP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0934
Polymers55,0013
Non-polymers921
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-36 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.820, 98.820, 81.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: catalytic core domain, UNP residues 1-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) PlysS / References: UniProt: Q9Y253, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*T*AP*CP*TP*TP*AP*TP*GP*AP*CP*GP*T)-3')


Mass: 3652.402 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*TP*AP*CP*GP*TP*CP*AP*TP*G)-3')


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG2K-MME, KCl, MES, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 18854 / Num. obs: 18824 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 33.64 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.27
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.35-2.415.080.7542.81408199.6
2.41-2.485.10.7053.051334199.6
2.48-2.555.110.5843.621313199.6
2.55-2.635.130.5184.081283199.8
2.63-2.715.120.4245.041232199.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MR2

3mr2


Resolution: 2.35→26.911 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8149 / SU ML: 0.29 / σ(F): 1.34 / σ(I): 0 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1462 7.77 %The same as 3MR2
Rwork0.1974 ---
all0.229 18844 --
obs0.2012 18820 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.59 Å2 / Biso mean: 23.1961 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→26.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 406 6 92 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084310
X-RAY DIFFRACTIONf_angle_d1.2785982
X-RAY DIFFRACTIONf_chiral_restr0.068676
X-RAY DIFFRACTIONf_plane_restr0.005645
X-RAY DIFFRACTIONf_dihedral_angle_d23.3261673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.4340.3041560.242317241880100
2.434-2.53140.34551710.241816981869100
2.5314-2.64650.29471440.226117241868100
2.6465-2.78590.28231420.212317321874100
2.7859-2.96020.27581420.205417371879100
2.9602-3.18840.2751330.198917571890100
3.1884-3.50870.21631370.175917321869100
3.5087-4.01490.23351540.1717241878100
4.0149-5.05290.19021340.172417651899100
5.0529-26.91270.24811490.22181765191499

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