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

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Basic information

Entry
Database: PDB / ID: 5ulx
TitleStructure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine crystallized in the presence of dCTP
Components
  • DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3')
  • DNA (5'-D(P*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')
  • DNA polymerase iota
KeywordsThansferase/DNA / human DNA polymerase iota N1-methyl-deoxyadenosine dCTP 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
DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / 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(P*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3')
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5094
Polymers52,4743
Non-polymers351
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.915, 97.915, 202.239
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: 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(P*(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)
#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
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 291 / 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: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 14 % PEG 5KMME, 0.4 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 41925 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rsym value: 0.074 / Net I/σ(I): 25.2
Reflection shellResolution: 1.96→2.02 Å / Num. unique all: 4084

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FLL

2fll


Resolution: 1.96→48.96 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.84
RfactorNum. reflection% reflection
Rfree0.239 3153 7.53 %
Rwork0.216 --
obs0.217 41847 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 306 1 291 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053202
X-RAY DIFFRACTIONf_angle_d0.6974404
X-RAY DIFFRACTIONf_dihedral_angle_d16.5731903
X-RAY DIFFRACTIONf_chiral_restr0.045529
X-RAY DIFFRACTIONf_plane_restr0.004513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9609-1.99010.29271430.27071613X-RAY DIFFRACTION99
1.9901-2.02120.31651290.27371653X-RAY DIFFRACTION100
2.0212-2.05440.29321310.2561652X-RAY DIFFRACTION100
2.0544-2.08980.26951390.24441659X-RAY DIFFRACTION100
2.0898-2.12780.24971320.23581646X-RAY DIFFRACTION100
2.1278-2.16870.26211480.22131630X-RAY DIFFRACTION100
2.1687-2.2130.24131070.22131686X-RAY DIFFRACTION100
2.213-2.26110.27771320.23681656X-RAY DIFFRACTION100
2.2611-2.31370.23351230.22761678X-RAY DIFFRACTION100
2.3137-2.37160.26391270.22961648X-RAY DIFFRACTION100
2.3716-2.43570.26761110.23151697X-RAY DIFFRACTION100
2.4357-2.50730.27031320.24671682X-RAY DIFFRACTION100
2.5073-2.58830.29431430.23691652X-RAY DIFFRACTION100
2.5883-2.68080.25941220.23391671X-RAY DIFFRACTION100
2.6808-2.78810.2471390.23111677X-RAY DIFFRACTION100
2.7881-2.9150.26381380.23261681X-RAY DIFFRACTION100
2.915-3.06860.29311360.23061696X-RAY DIFFRACTION100
3.0686-3.26090.25241480.21841689X-RAY DIFFRACTION100
3.2609-3.51260.20211480.19931685X-RAY DIFFRACTION100
3.5126-3.86590.22281500.19271700X-RAY DIFFRACTION100
3.8659-4.4250.22041600.17921711X-RAY DIFFRACTION100
4.425-5.57380.20951500.19481756X-RAY DIFFRACTION100
5.5738-48.97270.21771650.22221876X-RAY DIFFRACTION99

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