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- PDB-7lcd: Crystal structure of human polymerase eta complexed with syn N7-a... -

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Basic information

Entry
Database: PDB / ID: 7lcd
TitleCrystal structure of human polymerase eta complexed with syn N7-acetophenoneguanine
Components
  • DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')
  • DNA (5'-D(*CP*AP*T*(T0P)P*CP*TP*CP*AP*CP*AP*CP*T)-3')
  • DNA polymerase eta
KeywordsDNA BINDING PROTEIN/DNA / DNA lesion bypass / Translesion synthesis / Catalytic metals / syn-anti equilibrium / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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. ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsJung, H. / Lee, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of human polymerase eta complexed with syn N7-acetophenoneguanine
Authors: Jung, H. / Lee, S.
History
DepositionJan 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase eta
T: DNA (5'-D(*CP*AP*T*(T0P)P*CP*TP*CP*AP*CP*AP*CP*T)-3')
P: DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)54,5523
Polymers54,5523
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-27 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.785, 98.785, 81.876
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

#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
#2: DNA chain DNA (5'-D(*CP*AP*T*(T0P)P*CP*TP*CP*AP*CP*AP*CP*T)-3')


Mass: 3719.487 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES pH 6.5 20% PEG2000 MME 5 mM magnesium chloride

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 31506 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rpim(I) all: 0.057 / Net I/σ(I): 24.2
Reflection shellResolution: 1.98→2.01 Å / Mean I/σ(I) obs: 2.48 / Num. unique obs: 1580 / CC1/2: 0.755 / Rpim(I) all: 0.427 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3N

4o3n


Resolution: 1.98→42.78 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 1607 5.11 %
Rwork0.1823 --
obs0.1837 31450 99.81 %
Displacement parametersBiso mean: 33.57 Å2
Refinement stepCycle: LAST / Resolution: 1.98→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 377 0 211 3933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763821
X-RAY DIFFRACTIONf_angle_d0.9365230
X-RAY DIFFRACTIONf_chiral_restr0.0521588
X-RAY DIFFRACTIONf_plane_restr0.0049615
X-RAY DIFFRACTIONf_dihedral_angle_d27.24111484
LS refinement shellResolution: 1.98→2.05 Å
RfactorNum. reflection% reflection
Rfree0.2623 135 5.07 %
Rwork0.2196 2661 -
obs--98 %

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