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- PDB-4dl7: Human DNA polymerase eta fails to extend primer 2 nucleotide afte... -

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Basic information

Entry
Database: PDB / ID: 4dl7
TitleHuman DNA polymerase eta fails to extend primer 2 nucleotide after cisplatin crosslink (Pt-GG4).
Components
  • DNA (5'-D(*TP*AP*CP*TP*CP*GP*GP*TP*CP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*GP*AP*CP*CP*G)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA/INHIBITOR / cisplatin / chemoresistence / translesion synthesis / human DNA polymerse eta / kinetics / molecular splint / inhibition / DNA distorsion / second TLS polymerase / nucleotidyl transfer reaction / PCNA / TRANSFERASE-DNA-INHIBITOR 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 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 / 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
Cisplatin / Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsZhao, Y. / Biertumpfel, C. / Gregory, M. / Hua, Y. / Hanaoka, F. / Yang, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta
Authors: Zhao, Y. / Biertumpfel, C. / Gregory, M.T. / Hua, Y.J. / Hanaoka, F. / Yang, W.
History
DepositionFeb 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 13, 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 / 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(*TP*AP*CP*TP*CP*GP*GP*TP*CP*AP*CP*T)-3')
P: DNA (5'-D(*TP*AP*GP*TP*GP*AP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8696
Polymers54,9873
Non-polymers8823
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-29 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.000, 99.000, 81.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
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 (5'-D(*TP*AP*CP*TP*CP*GP*GP*TP*CP*AP*CP*T)-3')


Mass: 3613.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cisplatin-crosslinked oligonucleotide, chain T
#3: DNA chain DNA (5'-D(*TP*AP*GP*TP*GP*AP*CP*CP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide, chain P

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Non-polymers , 4 types, 330 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3
#6: Chemical ChemComp-CPT / Cisplatin / diammine(dichloro)platinum


Mass: 300.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl2H6N2Pt / Comment: medication, chemotherapy*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 41.62 %
Crystal growTemperature: 293 K / pH: 6
Details: MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2010
Details: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING
RadiationMonochromator: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 31415 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.67 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.09 / Net I/σ(I): 11.98
Reflection shellResolution: 1.97→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.12 / Rsym value: 0.45 / % possible all: 82.3

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MR2

3mr2


Resolution: 1.97→30 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.47 / σ(F): 1.35 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.214 2412 7.68 %
Rwork0.192 --
obs0.194 31395 97.9 %
all-32078 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.0972 Å2-0 Å2-0 Å2
2--1.0972 Å20 Å2
3----2.0483 Å2
Refinement stepCycle: LAST / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 390 20 327 4075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043962
X-RAY DIFFRACTIONf_angle_d0.8155448
X-RAY DIFFRACTIONf_dihedral_angle_d18.8871542
X-RAY DIFFRACTIONf_chiral_restr0.05614
X-RAY DIFFRACTIONf_plane_restr0.007637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.974-2.01430.2881150.28661384X-RAY DIFFRACTION80
2.0143-2.0580.29621480.23831671X-RAY DIFFRACTION97
2.058-2.10590.23631440.21781754X-RAY DIFFRACTION100
2.1059-2.15850.25691320.20711726X-RAY DIFFRACTION100
2.1585-2.21670.25441420.20241731X-RAY DIFFRACTION100
2.2167-2.28190.23571530.20561718X-RAY DIFFRACTION100
2.2819-2.35540.23641230.20531748X-RAY DIFFRACTION100
2.3554-2.43950.22241550.2011710X-RAY DIFFRACTION100
2.4395-2.5370.23121780.20571701X-RAY DIFFRACTION100
2.537-2.65220.24541410.19951743X-RAY DIFFRACTION100
2.6522-2.79160.22231420.19351737X-RAY DIFFRACTION100
2.7916-2.9660.20381400.20221747X-RAY DIFFRACTION100
2.966-3.19420.21681340.19041759X-RAY DIFFRACTION99
3.1942-3.5140.19641390.17211722X-RAY DIFFRACTION99
3.514-4.01890.18611500.15671714X-RAY DIFFRACTION98
4.0189-5.04970.14641280.16091721X-RAY DIFFRACTION97
5.0497-19.91370.20971480.19961697X-RAY DIFFRACTION95

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