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- PDB-3epi: Structure of Human DNA Polymerase Iota complexed with N2-ethylgua... -

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Basic information

Entry
Database: PDB / ID: 3epi
TitleStructure of Human DNA Polymerase Iota complexed with N2-ethylguanine and incoming TTP
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 iotaPOLI
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


translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...translesion synthesis / error-prone translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
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 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
PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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)58,1875
Polymers58,0693
Non-polymers1182
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)116,37310
Polymers116,1376
Non-polymers2364
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Unit cell
Length a, b, c (Å)98.643, 98.643, 202.231
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 / POLI / 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, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / 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: 2.45 Å3/Da / Density % sol: 49.71 %
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 SATURN 92 / Detector: CCD / Date: Apr 30, 2007
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→14.99 Å / Num. all: 13417 / Num. obs: 13417 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.44 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 26.36 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4 / % possible all: 100

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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: 2.9→14.99 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.852 / SU B: 35.863 / SU ML: 0.341 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28203 663 4.9 %RANDOM
Rwork0.23632 ---
obs0.23858 12753 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 310 6 69 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5322.1154547
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2695373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.52324.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45815562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9351519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022333
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21504
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22237
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3721.51879
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.71423037
X-RAY DIFFRACTIONr_scbond_it0.97731522
X-RAY DIFFRACTIONr_scangle_it1.6234.51510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 43 -
Rwork0.316 914 -
obs--100 %
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)
17.19630.13383.94983.68941.1956.4688-0.24960.25460.2823-0.47730.03090.614-0.5873-0.38810.2187-0.06450.03520.0627-0.208-0.0375-0.17624.8223-16.8769-19.8267
211.4432-2.261-0.93747.44440.966811.5902-0.2709-0.50830.48150.8052-0.25872.4454-0.3257-1.67980.52960.15110.10030.06070.4982-0.16410.7677-9.142-15.7086-19.9735
31.5788-0.3413-0.72481.5173-0.34463.6823-0.0388-0.0406-0.17940.0443-0.05360.01220.13330.01530.0923-0.1860.02250.0336-0.2045-0.0142-0.218911.5778-23.218-5.2161
47.3097-2.45070.78526.89940.53726.80520.50750.7537-0.3824-0.8682-0.15660.48240.3842-0.0107-0.35090.44450.1932-0.15550.09-0.17410.10937.4176-42.2074-34.1061
51.3108-2.1089-0.62295.0429-1.26543.4122-0.14820.1552-0.63440.0758-0.19690.36790.49190.15550.34510.01920.067-0.0175-0.0715-0.04620.07327.0008-39.0524-16.7689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 63
2X-RAY DIFFRACTION2A64 - 90
3X-RAY DIFFRACTION3A91 - 306
4X-RAY DIFFRACTION4A307 - 414
5X-RAY DIFFRACTION5C841 - 847
6X-RAY DIFFRACTION5B7 - 13

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