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- PDB-3tq1: Human DNA Polymerase eta in binary complex with DNA -

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Basic information

Entry
Database: PDB / ID: 3tq1
TitleHuman DNA Polymerase eta in binary complex with DNA
Components
  • DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*TP*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / Polymerase / DNA Replication / TRANSFERASE-DNA complex
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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 ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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 eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.556 Å
AuthorsUmmat, A. / Silverstein, T.D. / Jain, R. / Buku, A. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Human DNA Polymerase Eta Is Pre-Aligned for dNTP Binding and Catalysis.
Authors: Ummat, A. / Silverstein, T.D. / Jain, R. / Buku, A. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase eta
T: DNA (5'-D(*TP*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)55,3183
Polymers55,3183
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-31 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.914, 98.914, 81.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48645.762 Da / Num. of mol.: 1 / Fragment: catalytic core (UNP residues 1-432)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*TP*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3941.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20%-35% PEG 3350, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 14698 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.101 / Net I/σ(I): 14.6
Reflection shellResolution: 2.55→2.64 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.556→42.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 23.585 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24801 1104 7.5 %RANDOM
Rwork0.18616 ---
obs0.19086 13569 99.7 %-
all-13609 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å2-0 Å2
2--0.94 Å2-0 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.556→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3195 389 0 76 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223680
X-RAY DIFFRACTIONr_bond_other_d0.0010.022360
X-RAY DIFFRACTIONr_angle_refined_deg1.0342.0955058
X-RAY DIFFRACTIONr_angle_other_deg0.82935780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2795419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4323.923130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5031522
X-RAY DIFFRACTIONr_chiral_restr0.0540.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.52093
X-RAY DIFFRACTIONr_mcbond_other0.0441.5853
X-RAY DIFFRACTIONr_mcangle_it0.78123347
X-RAY DIFFRACTIONr_scbond_it0.83631587
X-RAY DIFFRACTIONr_scangle_it1.4324.51711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.556→2.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 82 -
Rwork0.234 966 -
obs--97.13 %
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)
1-0.0150.09640.0870.37880.11960.6958-0.0305-0.00970.03390.022-0.00880.05480.01750.00880.03930.20860.01160.00160.22020.0050.1947-15.856547.0655-2.934
20.59410.6-0.01341.8455-0.43390.9985-0.0906-0.0019-0.0413-0.18340.0258-0.11640.02830.01470.06480.15430.0050.03220.17420.02510.2035-18.252726.3422-15.878
30.5521-0.0184-0.43020.1716-0.10320.36840.0037-0.0057-0.01610.0130.010.0352-0.01510.0189-0.01370.1942-0.0196-0.00190.2040.00510.2134-30.250526.4761-7.6056
40.6828-0.65060.2472.15971.35142.178-0.2271-0.08090.0618-0.05440.03080.0487-0.0264-0.2330.19630.269-0.0483-0.03870.1753-0.01630.1527-28.703162.9742-18.5366
53.5038-2.355-1.67786.455-0.0223-0.6481-0.53410.24890.24051.59330.5713-0.2545-0.2001-0.1999-0.03720.480.0563-0.15030.22830.02810.0518-38.391650.0925-12.6259
61.97931.28360.61941.64180.89070.3824-0.05410.062-0.27290.11110.1017-0.11630.04330.0107-0.04770.1790.0066-0.00770.25430.03940.1742-33.396350.6993-11.0697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 93
2X-RAY DIFFRACTION2A94 - 160
3X-RAY DIFFRACTION3A161 - 313
4X-RAY DIFFRACTION4A314 - 432
5X-RAY DIFFRACTION5P2 - 9
6X-RAY DIFFRACTION6T3 - 13

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