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- PDB-6ui2: Structure of human DNA polymerase eta complexed with N7MG in the ... -

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Basic information

Entry
Database: PDB / ID: 6ui2
TitleStructure of human DNA polymerase eta complexed with N7MG in the template base paired with incoming non-hydrolyzable CTP
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*CP*AP*TP*(FMG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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
Chem-0KX / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKoag, M.C. / Lee, S.
CitationJournal: Molecules / Year: 2019
Title: Bypass of the Major Alkylative DNA Lesion by Human DNA Polymerase eta.
Authors: Koag, M.C. / Jung, H. / Kou, Y. / Lee, S.
History
DepositionSep 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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(*CP*AP*TP*(FMG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3477
Polymers54,7403
Non-polymers6074
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-43 kcal/mol
Surface area22180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.684, 98.684, 81.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48617.707 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules TP

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


Mass: 3695.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 97 molecules

#4: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M MES (pH 5.5), 5 mM MgCl2, and 15 to 20 % PEG 2K-MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.339→20 Å / Num. obs: 19191 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 19.15 Å2 / Rmerge(I) obs: 0.142 / Χ2: 1.075 / Net I/σ(I): 6.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.35-2.3911.30.4549420.6891100
2.39-2.4311.40.4429600.7211100
2.43-2.4811.40.4229600.7241100
2.48-2.5311.40.4269380.7271100
2.53-2.5911.40.3989480.7191100
2.59-2.6511.40.3419660.771100
2.65-2.7111.40.3159420.8021100
2.71-2.7911.40.2789660.8661100
2.79-2.8711.40.2439570.8611100
2.87-2.9611.40.2419420.9051100
2.96-3.0611.40.1969760.9911100
3.06-3.1911.40.1749551.0371100
3.19-3.3311.30.1399471.2221100
3.33-3.5111.30.1169651.4311100
3.51-3.7211.30.1059581.5861100
3.72-4.0111.20.0949561.7731100
4.01-4.4111.20.0829781.8841100
4.41-5.04110.0699611.4881100
5.04-6.31110.0739771.1621100
6.31-2011.20.059971.1651100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3N

4o3n


Resolution: 2.35→19.9 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.56
RfactorNum. reflection% reflection
Rfree0.2374 952 5.12 %
Rwork0.1704 --
obs0.1738 18602 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.26 Å2 / Biso mean: 24.9462 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 2.35→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 391 36 93 3886
Biso mean--13.81 26.49 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093896
X-RAY DIFFRACTIONf_angle_d1.5655348
X-RAY DIFFRACTIONf_chiral_restr0.121600
X-RAY DIFFRACTIONf_plane_restr0.006620
X-RAY DIFFRACTIONf_dihedral_angle_d21.6192301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.35-2.46190.25911390.173239493
2.4619-2.61580.28371350.1873242794
2.6158-2.81730.28021340.184249896
2.8173-3.09990.25581250.1875252997
3.0999-3.54620.26091240.1675258499
3.5462-4.45960.20611590.1502257699
4.4596-19.90.21360.1702264299

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