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- PDB-4fs1: Base pairing mechanism of N2,3-ethenoguanine with dTTP by human p... -

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Basic information

Entry
Database: PDB / ID: 4fs1
TitleBase pairing mechanism of N2,3-ethenoguanine with dTTP by human polymerase iota
Components
  • DNA 5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • DNA polymerase iotaPOLI
KeywordsTRANSFERASE/DNA / human DNA polymerase iota / DNA polymerase / DNA replication / lesion bypass / 2'-fluoro arabinose / N2 / 3-ethenoguanine / dTTP / template / 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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhao, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases.
Authors: Zhao, L. / Pence, M.G. / Christov, P.P. / Wawrzak, Z. / Choi, J.Y. / Rizzo, C.J. / Egli, M. / Guengerich, F.P.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_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_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
B: DNA 5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'
C: DNA 5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6758
Polymers58,0963
Non-polymers5785
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-66 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.470, 97.470, 203.541
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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DNA chain / Protein , 2 types, 3 molecules BCA

#1: DNA chain DNA 5'-D(*TP*CP*TP*(EFG)P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3'


Mass: 5534.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: site-specifically modified oligonucleotide
#2: Protein DNA polymerase iota / POLI / Eta2 / RAD30 homolog B


Mass: 47027.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD (DE3) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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Non-polymers , 4 types, 70 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 277 K / pH: 6.9
Details: 210 microM polymerase iota, 253 microM DNA complex, 10 mM MgCl2, 20 mM dTTP; mix 1:1 ratio with precipitant, 0.1 M MES (pH 6.5), 0.3 M (NH4)2SO4, 17% PEG 5000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 9, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→84.41 Å / Num. obs: 20822 / % possible obs: 99.8 % / Observed criterion σ(I): 2.75
Reflection shellResolution: 2.49→2.53 Å / % possible all: 100

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Processing

Software
NameVersionClassification
EMBL(with LS-CAT developed extensions)data collection
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→84.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.877 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.413 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1063 5.2 %RANDOM
Rwork0.215 ---
obs0.218 19448 99.7 %-
all-20575 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→84.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 328 33 65 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.9484642
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40424.839124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.41315553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8391519
X-RAY DIFFRACTIONr_chiral_restr0.1390.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212363
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 73 -
Rwork0.311 1224 -
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)
10.7077-0.7323-0.95242.95721.512.0233-0.07850.2560.16690.27480.0093-0.35580.1387-0.29490.06930.09430.0289-0.03430.1450.03670.235-4.72536.1462-19.6792
20.2164-0.09560.05480.7554-0.08930.4480.03730.04870.0438-0.0807-0.0739-0.15940.0639-0.06230.03660.06930.03880.01030.07150.01180.0391-7.288526.9974-15.2554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C839 - 847
2X-RAY DIFFRACTION2A26 - 414

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