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- PDB-3epg: Structure of Human DNA Polymerase Iota complexed with N2-ethylguanine -

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Basic information

Entry
Database: PDB / ID: 3epg
TitleStructure of Human DNA Polymerase Iota complexed with N2-ethylguanine
Components
  • 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
  • DNA polymerase iota
KeywordsTRANSFERASE/DNA / DNA pol iota / lesion bypass / N2-ethylguanine / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Nucleus / Schiff base / Transferase / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nuclear speck ...error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / 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 ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPence, M.G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Lesion bypass of N2-ethylguanine by human DNA polymerase iota.
Authors: Pence, M.G. / Blans, P. / Zink, C.N. / Hollis, T. / Fishbein, J.C. / Perrino, F.W.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_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 iota
B: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
C: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6288
Polymers58,0693
Non-polymers5595
Water1,24369
1
A: DNA polymerase iota
B: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
C: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
hetero molecules

A: DNA polymerase iota
B: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
C: 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,25516
Polymers116,1376
Non-polymers1,11810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Unit cell
Length a, b, c (Å)98.535, 98.535, 202.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein DNA polymerase iota / RAD30 homolog B / Eta2


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: Catalytic Fragment (UNP residues 1-420)
Source method: isolated from a genetically manipulated source
Details: MBP-DNA pol Iota Fusion with PreScission Protease cleavage site
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, POLI (amino acids 1-420), RAD30B / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta 2 cells / References: UniProt: Q9UNA4, DNA-directed DNA polymerase
#2: DNA chain 5'-D(*DTP*DCP*DTP*(2EG)P*DGP*DGP*DGP*DTP*DCP*DCP*DTP*DAP*DGP*DGP*DAP*DCP*DCP*(DOC))-3'


Mass: 5520.607 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: A self-annealing oligonucletoide was synthesized by Midland Certified Reagents containing N2-ethylgaunine using phosphoramidite chemistry
#3: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12-15% PEG MME 5000, 0.2-0.4M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG MME 500011
2Ammonium Sulfate11
3MES11
4PEG MME 500012
5Ammonium Sulfate12
6MES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 21, 2006 / Details: Confocal
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 30150 / Num. obs: 19625 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.77 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 13
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.73 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.1 / % possible all: 90.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ALZ minus DNA

2alz


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.885 / SU B: 22.59 / SU ML: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.427 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28284 1046 5.1 %RANDOM
Rwork0.23435 ---
obs0.23671 19625 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 310 32 69 3307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8062.1244513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.835371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71124.715123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23715527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281519
X-RAY DIFFRACTIONr_chiral_restr0.1380.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022310
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.21501
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22211
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2122
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4310.211
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5161.51869
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96823011
X-RAY DIFFRACTIONr_scbond_it1.57431498
X-RAY DIFFRACTIONr_scangle_it2.5194.51502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 71 -
Rwork0.363 1418 -
obs--99.87 %
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)
18.5998-0.31286.07954.7823-1.402211.1272-0.37450.10670.63460.5012-0.2793-1.3135-0.82671.27820.6539-0.062-0.11820.0016-0.05780.0980.0576-0.347-17.32721.351
22.09990.6249-1.21661.5517-0.6427.15190.02360.1450.0986-0.2308-0.10830.2046-0.3418-0.59950.0847-0.17520.03370.0287-0.2545-0.0272-0.2489-16.744-16.0963.829
31.04630.361-1.50720.7296-0.48314.1136-0.0402-0.2903-0.64590.1499-0.2969-0.49430.95150.52590.33710.172-0.04970.0436-0.03730.07890.1031-2.542-36.5419.398
47.39241.02613.719711.115-0.77876.31450.3159-0.6563-0.48360.92760.0439-0.05750.5091-0.4501-0.35970.3634-0.2715-0.1320.10860.2421-0.0323-9.62-43.01433.249
51.75540.6831-1.52943.4246-1.07646.2816-0.05550.0643-0.5171-0.2769-0.1009-0.29920.4946-0.160.1564-0.0904-0.0689-0.0403-0.09380.04260.0374-6.571-39.29316.679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 105
2X-RAY DIFFRACTION2A107 - 230
3X-RAY DIFFRACTION3A231 - 324
4X-RAY DIFFRACTION4A325 - 414
5X-RAY DIFFRACTION5C841 - 847
6X-RAY DIFFRACTION5B7 - 13

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