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- PDB-5ulw: Structure of human DNA polymerase iota bound to template 1-methyl... -

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Basic information

Entry
Database: PDB / ID: 5ulw
TitleStructure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine
Components
  • DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')
  • DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')
  • DNA polymerase iota
KeywordsThansferase/DNA / human DNA polymerase iota N1-methyl-deoxyadenosine dTTP TLS / Thansferase-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 replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...error-prone translesion synthesis / 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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.617 Å
AuthorsJain, R. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01-ES021452 United States
CitationJournal: Sci Rep / Year: 2017
Title: Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-iota.
Authors: Jain, R. / Choudhury, J.R. / Buku, A. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')
T: DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0166
Polymers52,4743
Non-polymers5423
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-32 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.918, 97.918, 202.473
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 , 2 types, 2 molecules PT

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


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#2: DNA chain DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')


Mass: 3355.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase iota / 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) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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Non-polymers , 4 types, 90 molecules

#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.0, 18 % PEG 5KMME, 0.4 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.62→50 Å / Num. obs: 18059 / % possible obs: 99.7 % / Redundancy: 14 % / Rsym value: 0.085 / Net I/σ(I): 27.9
Reflection shellResolution: 2.62→2.71 Å / Num. unique all: 1730 / % possible all: 69.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FLL

2fll


Resolution: 2.617→48.959 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 1419 7.88 %
Rwork0.2038 --
obs0.2074 18014 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.617→48.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2775 322 31 87 3215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083219
X-RAY DIFFRACTIONf_angle_d1.0084431
X-RAY DIFFRACTIONf_dihedral_angle_d17.7531897
X-RAY DIFFRACTIONf_chiral_restr0.051533
X-RAY DIFFRACTIONf_plane_restr0.005511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6172-2.71070.30391220.22981606X-RAY DIFFRACTION99
2.7107-2.81920.30451440.23961599X-RAY DIFFRACTION100
2.8192-2.94750.26731300.2411635X-RAY DIFFRACTION100
2.9475-3.10290.36021250.23441637X-RAY DIFFRACTION100
3.1029-3.29730.29411470.22551630X-RAY DIFFRACTION100
3.2973-3.55180.25391460.20071638X-RAY DIFFRACTION100
3.5518-3.90910.24911430.18921660X-RAY DIFFRACTION100
3.9091-4.47440.23271610.17971659X-RAY DIFFRACTION100
4.4744-5.6360.20121390.19091703X-RAY DIFFRACTION100
5.636-48.96750.22941620.20611828X-RAY DIFFRACTION100

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