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- PDB-4ed6: Human DNA polymerase eta - DNA ternary complex: Reaction in the A... -

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Basic information

Entry
Database: PDB / ID: 4ed6
TitleHuman DNA polymerase eta - DNA ternary complex: Reaction in the AT crystal at pH 6.7 for 15 hr, Sideway translocation
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/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
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.211 Å
AuthorsNakamura, T. / Zhao, Y. / Yang, W.
CitationJournal: Nature / Year: 2012
Title: Watching DNA polymerase eta make a phosphodiester bond
Authors: Nakamura, T. / Zhao, Y. / Yamagata, Y. / Hua, Y.J. / Yang, W.
History
DepositionMar 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1795
Polymers54,9953
Non-polymers1842
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-26 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.786, 98.786, 82.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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 (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(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')


Mass: 2739.824 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 6-17%(W/V) PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20425 / % possible obs: 89.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 16.15 Å2 / Rsym value: 0.11 / Net I/σ(I): 8.4
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.445 / % possible all: 78.1

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.211→24.012 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.8262 / SU ML: 0.33 / σ(F): 0.01 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 964 5.11 %
Rwork0.1978 --
obs0.2009 18862 82.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.288 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 72.86 Å2 / Biso mean: 20.5522 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.5028 Å20 Å2-0 Å2
2--0.5028 Å2-0 Å2
3----1.0055 Å2
Refinement stepCycle: LAST / Resolution: 2.211→24.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 408 12 225 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043922
X-RAY DIFFRACTIONf_angle_d0.8185381
X-RAY DIFFRACTIONf_chiral_restr0.051603
X-RAY DIFFRACTIONf_plane_restr0.003626
X-RAY DIFFRACTIONf_dihedral_angle_d16.6731516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2113-2.32780.31431140.25452092220668
2.3278-2.47350.2831270.23452356248376
2.4735-2.66420.32181310.22972442257379
2.6642-2.93190.28531320.22672610274284
2.9319-3.35520.2771450.1972736288188
3.3552-4.22350.21131550.15182855301092
4.2235-24.01310.20531600.16292807296789

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