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- PDB-8ski: Crystal structure of human DNA polymerase eta incorporating 5F-dU... -

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Basic information

Entry
Database: PDB / ID: 8ski
TitleCrystal structure of human DNA polymerase eta incorporating 5F-dUTP across HX
Components
  • DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')
  • DNA (5'-D(P*TP*IP*CP*TP*CP*AP*CP*AP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA damage / DNA replication / translesion synthesis / TRANSFERASE-DNA complex / anti-cancer / 5-FU
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 / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...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 / 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/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-B7P / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.163 Å
AuthorsJung, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA
Authors: Jung, H.
History
DepositionApr 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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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(P*TP*IP*CP*TP*CP*AP*CP*AP*CP*T)-3')
P: DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9265
Polymers54,3993
Non-polymers5262
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-32 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.560, 98.560, 81.094
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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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(P*TP*IP*CP*TP*CP*AP*CP*AP*CP*T)-3')


Mass: 3567.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')


Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 158 molecules

#4: Chemical ChemComp-B7P / 2'-deoxy-5-fluorouridine 5'-(tetrahydrogen triphosphate) / 5-FdUTP


Mass: 486.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14FN2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.163→58.791 Å / Num. obs: 24004 / % possible obs: 100 % / Redundancy: 13.43 % / Biso Wilson estimate: 38.02 Å2 / CC1/2: 0.9981 / Net I/σ(I): 9.665
Reflection shellResolution: 2.163→2.202 Å / Num. unique obs: 1260 / CC1/2: 0.4812

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4O3N

4o3n


Resolution: 2.163→32.26 Å / SU ML: 0.3416 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2493 1184 4.94 %
Rwork0.1996 22800 -
obs0.2021 23984 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.81 Å2
Refinement stepCycle: LAST / Resolution: 2.163→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 366 30 156 3889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913833
X-RAY DIFFRACTIONf_angle_d1.10475257
X-RAY DIFFRACTIONf_chiral_restr0.0512589
X-RAY DIFFRACTIONf_plane_restr0.0083614
X-RAY DIFFRACTIONf_dihedral_angle_d17.6539632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.163-2.260.32531590.25432817X-RAY DIFFRACTION99.97
2.26-2.380.31261560.23992819X-RAY DIFFRACTION100
2.38-2.530.33441570.23752849X-RAY DIFFRACTION100
2.53-2.720.29011080.23062861X-RAY DIFFRACTION99.93
2.72-30.28421580.2112855X-RAY DIFFRACTION100
3-3.430.23641560.20562824X-RAY DIFFRACTION99.97
3.43-4.320.20731220.17092887X-RAY DIFFRACTION100
4.32-32.260.22251680.18542888X-RAY DIFFRACTION99.77

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