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- PDB-3gv5: Human DNA polymerase iota in complex with T template DNA and inco... -

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Basic information

Entry
Database: PDB / ID: 3gv5
TitleHuman DNA polymerase iota in complex with T template DNA and incoming ddADP
Components
  • 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
  • 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
  • DNA polymerase iota
KeywordsTRANSFERASE/DNA / Y-family polymerase / polymerase iota / error prone replication / 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


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
2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKirouac, K.N. / Ling, H.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase iota
Authors: Kirouac, K.N. / Ling, H.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA polymerase iota
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
D: DNA polymerase iota
E: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
F: 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,74817
Polymers108,5456
Non-polymers1,20311
Water13,277737
1
B: DNA polymerase iota
P: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
T: 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9209
Polymers54,2723
Non-polymers6486
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-87 kcal/mol
Surface area20840 Å2
MethodPISA
2
D: DNA polymerase iota
E: 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'
F: 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8288
Polymers54,2723
Non-polymers5565
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-78 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.160, 71.750, 127.420
Angle α, β, γ (deg.)90.00, 112.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules BD

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


Mass: 47590.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Plasmid: pGST-parrallel1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules PETF

#2: DNA chain 5'-D(*GP*TP*GP*GP*AP*TP*GP*AP*G)-3'


Mass: 2835.871 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*CP*AP*TP*TP*CP*TP*CP*AP*TP*CP*CP*AP*C)-3'


Mass: 3846.525 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 4 types, 748 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ADI / 2',3'-DIDEOXYADENOSINE-5'-DIPHOSPHATE


Mass: 395.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O8P2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / 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: 2.73 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 15% PEG 3350, 0.15 M CaCl2, 5% glycerol, 0.005M DTT, pH 7.5, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98322 Å
DetectorDate: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98322 Å / Relative weight: 1
ReflectionResolution: 1.95→51.57 Å / Num. obs: 84496 / % possible obs: 99 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Χ2: 1.785 / Net I/σ(I): 24.607
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.983.10.61740901.02196.3
1.98-2.023.30.56541781.056197.9
2.02-2.063.50.46541301.077198.1
2.06-2.13.50.39941751.126198.8
2.1-2.153.60.32641841.18198.9
2.15-2.23.60.29741941.199198.8
2.2-2.253.60.26742381.283198.8
2.25-2.313.60.23542301.334199.2
2.31-2.383.70.19442061.41199.6
2.38-2.463.70.16942431.445199.5
2.46-2.543.70.14942341.593199.5
2.54-2.653.70.12542141.691199.5
2.65-2.773.70.10742361.924199.4
2.77-2.913.70.09342912.151199.8
2.91-3.13.70.07642112.414199.8
3.1-3.333.70.06242682.744199.6
3.33-3.673.60.05542823.192199.7
3.67-4.23.60.0542633.429199.5
4.2-5.293.50.03942902.547199.4
5.29-503.70.02443391.461198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2→51.57 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.964 / SU B: 8.812 / SU ML: 0.128 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.167
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1551 2.1 %RANDOM
Rwork0.205 ---
obs0.206 75523 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.39 Å2 / Biso mean: 58.903 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20.26 Å2
2---0.08 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 892 64 737 7695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227150
X-RAY DIFFRACTIONr_angle_refined_deg1.9582.1549832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.0195758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224.924264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.786151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5861537
X-RAY DIFFRACTIONr_chiral_restr0.1470.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214913
X-RAY DIFFRACTIONr_mcbond_it0.711.53805
X-RAY DIFFRACTIONr_mcangle_it1.29826179
X-RAY DIFFRACTIONr_scbond_it2.33933345
X-RAY DIFFRACTIONr_scangle_it3.2624.53653
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 101 -
Rwork0.23 4886 -
all-4987 -
obs--86.96 %
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)
10.6538-0.1270.06434.2599-0.53880.74190.08650.14440.016-0.5285-0.05980.18740.09840.0682-0.0267-0.35330.0183-0.0207-0.4613-0.0002-0.67774.59164.61633.712
21.7974-0.11310.73423.6244-0.89241.9490.08690.03520.0846-0.71720.09740.93510.3312-0.1325-0.1843-0.3512-0.0328-0.2316-0.52330.0387-0.489760.32171.09330.509
32.51021.5569-0.03752.1393-1.19061.16160.0839-0.07360.04010.2345-0.06630.4141-0.1953-0.2568-0.0176-0.5049-0.03620.0736-0.4564-0.0824-0.489558.92371.29354.077
42.51580.97250.8015.91670.49193.0363-0.08080.12020.20550.31040.0662-0.6341-0.03530.3530.0146-0.45270.0173-0.1307-0.4782-0.0075-0.579193.25366.9658.193
51.06610.632-0.79261.0667-0.60770.76350.1235-0.12670.0810.1154-0.0829-0.0613-0.01130.1181-0.0406-0.4213-0.0281-0.056-0.47740.0111-0.614998.93837.19324.657
62.13930.254-0.55221.0015-0.50532.21320.10770.01730.06310.1529-0.03240.1002-0.09430.0353-0.0753-0.3825-0.0226-0.0138-0.51230.0076-0.670384.23630.89626.381
76.6961-1.09411.31031.2724-1.44111.85780.00090.51640.0271-0.16910.0905-0.09070.2421-0.3466-0.0914-0.45480.0038-0.0686-0.364-0.0745-0.737582.38929.1813.922
82.47090.3204-0.46434.13010.85953.3145-0.0427-0.083-0.2385-0.13490.1196-0.68530.20280.3573-0.0768-0.4451-0.00290.0611-0.4343-0.0056-0.4738117.43234.121.126
90.1066-0.3206-0.28551.24860.30751.83080.07580.04230.08670.146-0.1476-0.11250.0751-0.2520.0717-0.4151-0.0457-0.0054-0.4384-0.0673-0.573876.05168.89356.996
100.38060.2918-0.01590.3473-0.26590.52190.0260.0294-0.02080.0078-0.0336-0.14710.0327-0.10640.0076-0.21490.0319-0.0162-0.249-0.0464-0.3353100.43432.2141.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B28 - 155
2X-RAY DIFFRACTION2B156 - 235
3X-RAY DIFFRACTION3B236 - 301
4X-RAY DIFFRACTION4B302 - 414
5X-RAY DIFFRACTION5D28 - 151
6X-RAY DIFFRACTION6D152 - 242
7X-RAY DIFFRACTION7D243 - 299
8X-RAY DIFFRACTION8D300 - 414
9X-RAY DIFFRACTION9P865 - 873
10X-RAY DIFFRACTION9T837 - 849
11X-RAY DIFFRACTION10E865 - 873
12X-RAY DIFFRACTION10F837 - 849

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