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- PDB-4j9n: Human DNA polymerase eta-DNA ternary complex: misincorporation G ... -

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Basic information

Entry
Database: PDB / ID: 4j9n
TitleHuman DNA polymerase eta-DNA ternary complex: misincorporation G opposite T after a G at the primer 3' end (GA/G)
Components
  • (DNA) x 2
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / immunoglobulin / A to G transition / misincorporation / wobble base pair / DNA polymerase / DNA / 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-XG4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.956 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 / 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_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.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.pdbx_dist_value / _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_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
P: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7268
Polymers54,9873
Non-polymers7395
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-44 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.664, 98.664, 81.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 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

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA


Mass: 3613.366 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 331 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 41.27 %
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: Aug 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 32840 / Num. obs: 32381 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 18.22 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.95-1.986.30.4264.8216281100
1.98-2.026.40.3835.411628199.5
2.02-2.066.30.3326.321619199.3
2.06-2.16.40.2877.451641199.3
2.1-2.156.30.2568.161632199.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MR2

3mr2


Resolution: 1.956→28.482 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8883 / SU ML: 0.2 / σ(F): 1.36 / σ(I): 0 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 1643 5.07 %The same as 3MR2
Rwork0.1646 ---
all0.183 32810 --
obs0.1663 32375 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.91 Å2 / Biso mean: 21.8581 Å2 / Biso min: 3.68 Å2
Refinement stepCycle: LAST / Resolution: 1.956→28.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 362 45 326 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014034
X-RAY DIFFRACTIONf_angle_d1.2295549
X-RAY DIFFRACTIONf_chiral_restr0.078621
X-RAY DIFFRACTIONf_plane_restr0.006648
X-RAY DIFFRACTIONf_dihedral_angle_d19.7211575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9556-2.01310.24091360.17712561269799
2.0131-2.07810.25781390.167725542693100
2.0781-2.15230.21121600.16172563272399
2.1523-2.23840.21781380.160125422680100
2.2384-2.34030.20071540.16142581273599
2.3403-2.46360.2181300.16772589271999
2.4636-2.61780.22661530.17742520267399
2.6178-2.81980.23621240.17512573269799
2.8198-3.10330.19361330.17652565269899
3.1033-3.55160.20991350.15382552268798
3.5516-4.47180.14251160.14422561267798
4.4718-28.48490.171250.17582571269696

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