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- PDB-3g6v: DNA synthesis across an abasic lesion by human DNA polymerase-iota -

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Basic information

Entry
Database: PDB / ID: 3g6v
TitleDNA synthesis across an abasic lesion by human DNA polymerase-iota
Components
  • DNA polymerase iota
  • Primer DNA strand
  • Template DNA strand
KeywordsREPLICATION/DNA / DNA Polymerase / Y-family / Lesion Bypass / abasic site / ternary complex / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Magnesium / Metal-binding / Mutator protein / Nucleotidyltransferase / Nucleus / Schiff base / Transferase / REPLICATION-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
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
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNair, D.T. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2009
Title: DNA Synthesis across an Abasic Lesion by Human DNA Polymerase iota
Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionFeb 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 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.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.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
A: DNA polymerase iota
P: Primer DNA strand
T: Template DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1956
Polymers52,6393
Non-polymers5563
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-17 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.150, 98.150, 203.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe asymmetric unit of the crystal structure contains one biological unit.

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Components

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Protein , 1 types, 1 molecules A

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


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 / Plasmid: PBJ941 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5464 / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain Primer DNA strand


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide synthesis
#3: DNA chain Template DNA strand


Mass: 3520.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Oligonucleotide synthesis

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Non-polymers , 3 types, 174 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals grew over a period of one day, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 5, 2005 / Details: Si(111) double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 30070 / Num. obs: 29220 / % possible obs: 97 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 37.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 37.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
AMoREphasing
CNS1.1refinement
JDirectordata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FLL

2fll


Resolution: 2.2→39.22 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.481 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25146 2347 8 %RANDOM
Rwork0.21078 ---
obs0.21399 26873 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 311 32 171 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223291
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2662.1134505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97124.839124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.27115543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.7141519
X-RAY DIFFRACTIONr_chiral_restr0.1620.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212306
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21365
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22140
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2203
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.51860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93922998
X-RAY DIFFRACTIONr_scbond_it3.25431431
X-RAY DIFFRACTIONr_scangle_it4.7244.51507
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 149 -
Rwork0.224 1857 -
obs--92.36 %
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)
10.50480.11450.1630.7430.35051.83190.06950.0295-0.01-0.0354-0.0785-0.02530.11420.17060.0090.11170.023-0.02410.08140.00150.008916.117916.85425.9435
27.0805-0.8933-1.39766.39711.69436.21660.07370.1067-0.55150.4637-0.39411.22390.634-0.53720.32040.1562-0.14970.10790.1538-0.11260.2719-4.694816.165323.6626
36.401-0.87523.41411.61-0.11613.485-0.7038-0.16721.1886-0.0125-0.0732-0.0693-0.413-0.26550.7770.20190.0478-0.19370.0525-0.06180.26230.42635.1639-3.6848
44.67413.6445-2.32759.73710.30634.52241.3028-0.76471.36541.693-0.71681.3781-0.49240.4353-0.5860.5568-0.22850.43490.2143-0.29980.51487.295341.138432.9277
54.28180.3575-0.71392.85960.37731.19520.1330.05641.0192-0.0792-0.08180.656-0.06120.2103-0.05120.1344-0.0510.00350.08530.00390.3735.505237.416516.9507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 37
2X-RAY DIFFRACTION1A99 - 224
3X-RAY DIFFRACTION2A38 - 98
4X-RAY DIFFRACTION3A225 - 287
5X-RAY DIFFRACTION4A298 - 414
6X-RAY DIFFRACTION5P867 - 873
7X-RAY DIFFRACTION5T840 - 847

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