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- PDB-3gv8: Human DNA polymerase iota in complex with T template DNA and inco... -

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Basic information

Entry
Database: PDB / ID: 3gv8
TitleHuman DNA polymerase iota in complex with T template DNA and incoming dGTP
Components
  • 5'-D(*AP*GP*GP*AP*CP*CP*C)-3'
  • 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3'
  • DNA polymerase iotaPOLI
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


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
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_dist_value / _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
B: DNA polymerase iota
T: 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3'
P: 5'-D(*AP*GP*GP*AP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4376
Polymers51,8823
Non-polymers5563
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-41 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.070, 98.070, 203.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules B

#1: Protein DNA polymerase iota / POLI / 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: 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, 2 molecules TP

#2: DNA chain 5'-D(*AP*TP*GP*GP*GP*TP*CP*CP*T)-3'


Mass: 2746.809 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*GP*GP*AP*CP*CP*C)-3'


Mass: 2107.413 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 243 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growMethod: hanging drop / pH: 6.5
Details: 15% PEG 5000MME, 0.2M NH4SO4, 0.1M MES 6.5, 5% glycerol, hanging drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDate: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 40059 / % possible obs: 99.7 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.121 / Χ2: 5.148 / Net I/σ(I): 57.94
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.078.90.57738990.721100
2.07-2.1512.20.42939350.9471100
2.15-2.2514.30.33639331.2031100
2.25-2.3714.30.28439615.1561100
2.37-2.5214.30.22439692.2051100
2.52-2.7114.20.18939763.2851100
2.71-2.9914.20.16540114.9451100
2.99-3.42140.14240268.784199.9
3.42-4.3113.80.128409213.143199.9
4.31-5012.70.08342578.765197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2→23.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.805 / SU B: 7.384 / SU ML: 0.113 / SU R Cruickshank DPI: 0.171 / SU Rfree: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 826 2.1 %RANDOM
Rwork0.218 ---
obs0.219 39636 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.41 Å2 / Biso mean: 43.899 Å2 / Biso min: 23.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å20 Å2
2---0.43 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 320 33 240 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223338
X-RAY DIFFRACTIONr_angle_refined_deg1.8212.1164585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1924.298121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03715542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6141519
X-RAY DIFFRACTIONr_chiral_restr0.1350.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212328
X-RAY DIFFRACTIONr_mcbond_it0.8991.51871
X-RAY DIFFRACTIONr_mcangle_it1.61423023
X-RAY DIFFRACTIONr_scbond_it2.55831467
X-RAY DIFFRACTIONr_scangle_it3.8364.51562
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 87 -
Rwork0.259 2750 -
all-2837 -
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)
12.06740.041.56313.70371.08153.2699-0.11430.09140.1771-0.4261-0.31270.5946-0.6166-0.07360.4270.0630.1092-0.02290.0367-0.0629-0.16853.62-16.967-20.169
27.74430.18251.36898.40015.03859.2179-0.0133-0.50140.32480.0967-0.97182.4773-0.2595-1.59780.98510.03160.1027-0.07680.1119-0.1730.3649-8.983-16.329-22.032
30.9378-0.0238-0.55831.27420.08791.88450.0008-0.0454-0.04140.125-0.120.01650.01620.21440.11920.0330.02980.05160.0140.008-0.253311.697-23.295-3.831
42.86560.8023-0.98079.5311-0.11965.01360.4340.0684-0.7447-1.1486-0.41810.030.26720.2368-0.01590.23550.2065-0.1253-0.0607-0.206-0.14446.284-42.099-34.572
50.03020.12450.09941.65710.28040.3417-0.01240.1276-0.09430.1584-0.15410.30670.07060.14170.16640.0720.06750.03730.0062-0.0476-0.09775.111-38.1437-17.3402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B26 - 67
2X-RAY DIFFRACTION2B68 - 97
3X-RAY DIFFRACTION3B98 - 301
4X-RAY DIFFRACTION4B302 - 414
5X-RAY DIFFRACTION5T839 - 847
6X-RAY DIFFRACTION5P867 - 973

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