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- PDB-3gv7: Human DNA polymerase iota in complex with T template DNA and inco... -

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Basic information

Entry
Database: PDB / ID: 3gv7
TitleHuman DNA polymerase iota in complex with T template DNA and incoming dTTP
Components
  • 5'-D(*AP*GP*GP*AP*CP*CP*C)-3'
  • 5'-D(P*AP*TP*GP*GP*GP*TP*CP*CP*T)-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
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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 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 1.2Feb 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.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(P*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)52,4126
Polymers51,8823
Non-polymers5313
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-41 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.190, 97.190, 201.940
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 / 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(P*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, 268 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
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: 2.2→27.04 Å / Num. obs: 29366

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.2→27.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.807 / SU B: 11.241 / SU ML: 0.155 / SU R Cruickshank DPI: 0.245 / SU Rfree: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 604 2.1 %RANDOM
Rwork0.209 ---
obs0.21 28762 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: 105.64 Å2 / Biso mean: 50.342 Å2 / Biso min: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0.2 Å20 Å2
2---0.41 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 322 31 265 3596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223411
X-RAY DIFFRACTIONr_angle_refined_deg1.5572.1174669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55724.848132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.02115589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0981519
X-RAY DIFFRACTIONr_chiral_restr0.120.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212375
X-RAY DIFFRACTIONr_mcbond_it0.6531.51880
X-RAY DIFFRACTIONr_mcangle_it1.2923055
X-RAY DIFFRACTIONr_scbond_it2.02631531
X-RAY DIFFRACTIONr_scangle_it3.1554.51614
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 46 -
Rwork0.275 2068 -
all-2114 -
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)
13.37960.07062.91443.70470.49455.7664-0.1636-0.06520.4019-0.3607-0.28620.9471-0.9014-0.54260.44980.03350.1981-0.05040.0338-0.07480.0188-1.286-16.825-21.563
21.75020.25990.17732.5711.49915.69470.060.01610.03090.1276-0.1354-0.2386-0.13350.62420.07540.0238-0.04770.0580.0150.0988-0.168719.816-17.221-6.927
31.4306-0.1785-0.73910.52010.16572.1874-0.0710.0354-0.13260.1122-0.09970.0170.05590.08630.17080.02990.02980.0815-0.0199-0.0092-0.20297.81-25.838-0.87
40.719-1.6429-1.65299.44630.73115.42960.53480.0988-0.3027-1.2048-0.47770.0880.41340.3069-0.05710.34070.188-0.10950.0064-0.206-0.24985.994-41.726-34.169
50.13680.10.42294.23490.37111.30760.04910.2654-0.31640.2607-0.28870.72660.37910.18980.23960.10370.14870.07010.0409-0.0842-0.05644.631-37.914-17.215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B26 - 102
2X-RAY DIFFRACTION2B103 - 162
3X-RAY DIFFRACTION3B163 - 299
4X-RAY DIFFRACTION4B300 - 414
5X-RAY DIFFRACTION5T839 - 847
6X-RAY DIFFRACTION5P867 - 973

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