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- PDB-4dl3: Human DNA polymerase eta inserting dCMPNPP opposite GG template (... -

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Basic information

Entry
Database: PDB / ID: 4dl3
TitleHuman DNA polymerase eta inserting dCMPNPP opposite GG template (GG0b).
Components
  • DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*C)-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 / nucleus / 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 / response to radiation ...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 / response to radiation / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / site of double-strand break / damaged DNA binding / DNA-directed DNA polymerase / 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
Chem-0KX / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.1Jun 26, 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 / 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_asym_id / _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.ptnr3_auth_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_conn.ptnr2_label_seq_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
A: DNA polymerase eta
T: DNA (5'-D(*TP*AP*CP*GP*GP*TP*CP*AP*CP*AP*CP*T)-3')
P: DNA (5'-D(*TP*AP*GP*TP*GP*TP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8029
Polymers55,0113
Non-polymers7916
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-47 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.380, 97.380, 81.000
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 / Fragment: 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

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DNA chain , 2 types, 2 molecules TP

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


Mass: 3622.380 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*TP*GP*AP*C)-3')


Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: oligonucleotide, chain P

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Non-polymers , 4 types, 283 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.02 Å3/Da / Density % sol: 38.97 %
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: 2.1→30 Å / Num. obs: 25209 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23.71 Å2 / Rmerge(I) obs: 0.171 / Rsym value: 0.096 / Net I/σ(I): 12.73
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.47 / Rsym value: 0.576 / % possible all: 97.7

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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: 2.1→30 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.59 / σ(F): 1.34 / Phase error: 21.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 1950 7.74 %
Rwork0.204 --
obs0.205 25208 98.8 %
all-25529 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.49 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.2808 Å20 Å2-0 Å2
2--0.2808 Å20 Å2
3---1.0062 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 392 48 277 4083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043972
X-RAY DIFFRACTIONf_angle_d0.7515464
X-RAY DIFFRACTIONf_dihedral_angle_d20.381562
X-RAY DIFFRACTIONf_chiral_restr0.048612
X-RAY DIFFRACTIONf_plane_restr0.005626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15250.29441470.26211623X-RAY DIFFRACTION98
2.1525-2.21070.28121420.25221641X-RAY DIFFRACTION98
2.2107-2.27560.28871180.25231648X-RAY DIFFRACTION98
2.2756-2.34890.25931290.22441661X-RAY DIFFRACTION98
2.3489-2.43270.23741680.23151629X-RAY DIFFRACTION99
2.4327-2.530.27951550.23531621X-RAY DIFFRACTION98
2.53-2.64480.24841330.23911664X-RAY DIFFRACTION99
2.6448-2.78390.23031440.22471659X-RAY DIFFRACTION99
2.7839-2.95780.24731320.21681686X-RAY DIFFRACTION99
2.9578-3.18520.20591250.20581671X-RAY DIFFRACTION99
3.1852-3.50410.19771380.18751684X-RAY DIFFRACTION99
3.5041-4.00730.18151430.16631659X-RAY DIFFRACTION100
4.0073-5.03430.15951290.16261712X-RAY DIFFRACTION100
5.0343-200.19381470.20081700X-RAY DIFFRACTION99

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