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- PDB-2r8j: Structure of the Eukaryotic DNA Polymerase eta in complex with 1,... -

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Basic information

Entry
Database: PDB / ID: 2r8j
TitleStructure of the Eukaryotic DNA Polymerase eta in complex with 1,2-d(GpG)-cisplatin containing DNA
Components
  • DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')
  • DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')
  • DNA polymerase eta
KeywordsREPLICATION / TRANSFERASE/DNA / protein-cisplatin-DNA-dNTP complex / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase ...Translesion Synthesis by POLH / Termination of translesion DNA synthesis / mitotic sister chromatid cohesion / error-free translesion synthesis / error-prone translesion synthesis / replication fork / chromosome segregation / response to radiation / site of double-strand break / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / mitochondrion / zinc ion binding / nucleus
Similarity search - Function
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 ...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
Cisplatin / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCarell, T. / Alt, A. / Lammens, K.
CitationJournal: Science / Year: 2007
Title: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta
Authors: Alt, A. / Lammens, K. / Chiocchini, C. / Lammens, A. / Pieck, J.C. / Kuch, D. / Hopfner, K.P. / Carell, T.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_asym_id / _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
Q: DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')
U: DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')
P: DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')
T: DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')
A: DNA polymerase eta
B: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,19014
Polymers137,4966
Non-polymers1,6958
Water2,180121
1
Q: DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')
U: DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')
A: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5957
Polymers68,7483
Non-polymers8474
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
P: DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')
T: DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')
B: DNA polymerase eta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5957
Polymers68,7483
Non-polymers8474
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.090, 104.090, 293.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA chain , 2 types, 4 molecules QPUT

#1: DNA chain DNA (5'-D(*DGP*DTP*DGP*DGP*DAP*DTP*DGP*DAP*DG)-3')


Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYN
#2: DNA chain DNA (5'-D(P*DGP*DGP*DCP*DTP*DCP*DAP*DTP*DCP*DCP*DAP*DC)-3')


Mass: 3294.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYN

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Protein , 1 types, 2 molecules AB

#3: Protein DNA polymerase eta / E.C.2.7.7.7 / Radiation sensitive protein 30


Mass: 62617.781 Da / Num. of mol.: 2 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Details: MAN
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YPH499 (ATCC 76625) / Gene: RAD30, DBH1 / Plasmid: pExp007 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 Rosetta / References: UniProt: Q04049, DNA-directed DNA polymerase

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Non-polymers , 4 types, 129 molecules

#4: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 170 mM Calcium chloride, 16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1CaCl211
2PEG 335011
3CaCl212
4PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 30191 / Num. obs: 30191 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 40.053 Å2 / Rsym value: 0.154 / Net I/σ(I): 16.98
Reflection shellHighest resolution: 3.1 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 5.71 / Rsym value: 0.443 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JIH

1jih


Resolution: 3.1→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2574 2412 12.4 %random
Rwork0.2082 ---
all-30031 --
obs-30031 99.6 %-
Displacement parametersBiso mean: 33.1 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8103 818 66 121 9108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.20265
X-RAY DIFFRACTIONc_bond_d0.00415
X-RAY DIFFRACTIONc_mcbond_it1.3441.5
X-RAY DIFFRACTIONc_mcangle_it2.3722
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.152.5

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