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- PDB-3mfi: DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer -

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Basic information

Entry
Database: PDB / ID: 3mfi
TitleDNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer
Components
  • 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'
  • 5'-D(*TP*AP*AP*(TTD)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA damage / DNA repair / DNA replication / DNA synthesis / Nucleus / DNA-binding / Magnesium / Metal-binding / DNA-directed DNA Polymerase / Mutator protein / Nucleotidyltransferase / DNA POLYMERASE ETA / PROTEIN-DNA COMPLEX / THYMIDINE DIMER / CPD / UV-DAMAGE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


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 replication / damaged DNA binding / DNA-directed DNA polymerase ...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 replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / metal 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 / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain ...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 / 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsSilverstein, T.D. / Johnson, R.E. / Jain, R. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: Nature / Year: 2010
Title: Structural basis for the suppression of skin cancers by DNA polymerase eta.
Authors: Silverstein, T.D. / Johnson, R.E. / Jain, R. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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.pdbx_leaving_atom_flag / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 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

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase eta
P: 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'
T: 5'-D(*TP*AP*AP*(TTD)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7788
Polymers67,0463
Non-polymers7325
Water12,773709
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-66 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.087, 226.962, 85.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / / Radiation-sensitive protein 30


Mass: 58813.402 Da / Num. of mol.: 1 / Fragment: UNP residues 1-513 / Mutation: K140A,S144W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DBH1, RAD30, YDR419W / Plasmid: pSL414 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q04049, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'


Mass: 3205.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide
#3: DNA chain 5'-D(*TP*AP*AP*(TTD)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'


Mass: 5027.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide

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Non-polymers , 4 types, 714 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 3.22 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 33% PEG 4000, 0.1 M TRIS, 0.2 M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2008
RadiationMonochromator: Kohzu HLD8-24 Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 85689 / Num. obs: 85518 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.76-1.826.90.66599.6
1.82-1.97.20.48999.8
1.9-1.987.20.33699.9
1.98-2.097.30.24499.9
2.09-2.227.30.177100
2.22-2.397.30.148100
2.39-2.637.40.129100
2.63-3.017.40.115100
3.01-3.797.30.107100
3.79-507.10.09699.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JIH

1jih


Resolution: 1.76→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.501 / SU ML: 0.053 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18721 4273 5 %RANDOM
Rwork0.16354 ---
obs0.16475 81185 99.68 %-
all-85732 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.31 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.76→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 508 42 709 5294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224831
X-RAY DIFFRACTIONr_bond_other_d0.0010.023121
X-RAY DIFFRACTIONr_angle_refined_deg1.592.1116665
X-RAY DIFFRACTIONr_angle_other_deg0.90237688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67825188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73115773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5811519
X-RAY DIFFRACTIONr_chiral_restr0.090.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02876
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7141.52607
X-RAY DIFFRACTIONr_mcbond_other0.1781.51052
X-RAY DIFFRACTIONr_mcangle_it1.3924233
X-RAY DIFFRACTIONr_scbond_it2.10632224
X-RAY DIFFRACTIONr_scangle_it3.3154.52421
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.758→1.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 291 -
Rwork0.257 5768 -
obs--97.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2276-0.226-0.26280.81870.62610.6679-0.00240.0204-0.0566-0.0231-0.0414-0.04760.0207-0.03580.04380.09860.00730.02360.08480.00870.1047-18.965636.26690.6594
20.311-0.7028-0.69824.0862.88762.9963-0.0478-0.0946-0.09170.0453-0.0011-0.18970.1741-0.03160.04880.09530.01550.02290.07540.0410.1379-15.916825.26632.2764
30.37-0.068-0.07650.45470.26220.68950.00550.00680.0294-0.0082-0.0045-0.0418-0.04790.0279-0.00090.0671-0.00990.00270.10050.0070.0765-23.867955.062113.1149
42.1961-0.6090.48881.038-0.4690.74550.09370.0548-0.2119-0.0181-0.06980.2123-0.0209-0.0198-0.02390.05270.0113-0.01420.0967-0.0210.0994-47.807548.3050.2782
50.6570.71330.80221.42050.58132.29750.0212-0.0249-0.04260.0656-0.03610.13750.0334-0.07380.01490.11290.01650.01550.007-0.00260.0969-31.666212.92284.1704
61.9771-0.0747-1.32523.4663-1.2791.4002-0.0241-0.40480.1157-0.0670.0624-0.01620.06170.2575-0.03830.0897-0.0346-0.00790.1053-0.0310.1367-43.656324.27244.5267
71.15280.7357-0.55810.7702-0.25820.3113-0.21610.12430.2602-0.1380.25590.26280.1335-0.026-0.03990.0946-0.0272-0.02180.11660.02690.1824-40.320424.32051.0457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2A105 - 149
3X-RAY DIFFRACTION3A150 - 306
4X-RAY DIFFRACTION4A307 - 388
5X-RAY DIFFRACTION5A389 - 512
6X-RAY DIFFRACTION6DP - P1 - 11
7X-RAY DIFFRACTION7T4 - 16

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