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- PDB-5ewg: Ternary complex of human DNA polymerase eta inserting rATP opposi... -

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Basic information

Entry
Database: PDB / ID: 5ewg
TitleTernary complex of human DNA polymerase eta inserting rATP opposite an 8-Oxodeoxyguanosine Lesion
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*CP*AP*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / Polymerase-DNA Complex / ribonucleotide incorporation / 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-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / zinc ion binding / nucleoplasm / nucleus / 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
ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSu, Y. / Egli, M. / Guengerich, F.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES010375 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA160032 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Mechanism of Ribonucleotide Incorporation by Human DNA Polymerase eta.
Authors: Su, Y. / Egli, M. / Guengerich, F.P.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*(8OG)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)55,2705
Polymers54,7233
Non-polymers5472
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-39 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.024, 99.024, 81.571
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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 / Fragment: 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
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*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3678.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.) synthetic construct (others)

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Non-polymers , 3 types, 360 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaMES (pH 6.0), polyethylene glycol monomethyl ether 2000, and calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 45786 / % possible obs: 99.8 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3P

4o3p


Resolution: 1.75→42.325 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.215 2283 4.96 %
Rwork0.1781 --
obs0.18 45767 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→42.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 390 32 358 4009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073844
X-RAY DIFFRACTIONf_angle_d1.0235316
X-RAY DIFFRACTIONf_dihedral_angle_d15.8472280
X-RAY DIFFRACTIONf_chiral_restr0.055605
X-RAY DIFFRACTIONf_plane_restr0.005617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7495-1.76940.27781460.27662788X-RAY DIFFRACTION96
1.7694-1.79020.24131300.26582829X-RAY DIFFRACTION100
1.7902-1.8120.34381260.24932904X-RAY DIFFRACTION100
1.812-1.8350.29771740.25232872X-RAY DIFFRACTION100
1.835-1.85910.26451660.23932850X-RAY DIFFRACTION100
1.8591-1.88460.29731580.22452829X-RAY DIFFRACTION100
1.8846-1.91150.28011680.23422798X-RAY DIFFRACTION100
1.9115-1.94010.30441540.22072930X-RAY DIFFRACTION100
1.9401-1.97040.24421600.20862841X-RAY DIFFRACTION100
1.9704-2.00270.23981500.20532870X-RAY DIFFRACTION100
2.0027-2.03720.25241660.20032790X-RAY DIFFRACTION100
2.0372-2.07420.24711680.20182826X-RAY DIFFRACTION100
2.0742-2.11410.26261900.19442859X-RAY DIFFRACTION100
2.1141-2.15730.22561420.19192856X-RAY DIFFRACTION100
2.1573-2.20420.28351380.192919X-RAY DIFFRACTION100
2.2042-2.25550.26531540.18882837X-RAY DIFFRACTION100
2.2555-2.31190.19441620.18092795X-RAY DIFFRACTION100
2.3119-2.37440.18511640.17852884X-RAY DIFFRACTION100
2.3744-2.44420.21141420.17492849X-RAY DIFFRACTION100
2.4442-2.52310.2481200.18332901X-RAY DIFFRACTION100
2.5231-2.61330.21831480.19112882X-RAY DIFFRACTION100
2.6133-2.71790.22891220.18482853X-RAY DIFFRACTION100
2.7179-2.84160.25831220.18422878X-RAY DIFFRACTION100
2.8416-2.99130.27731360.19132885X-RAY DIFFRACTION100
2.9913-3.17870.21931010.19662896X-RAY DIFFRACTION100
3.1787-3.4240.22991780.16432842X-RAY DIFFRACTION100
3.424-3.76840.15281240.15252860X-RAY DIFFRACTION100
3.7684-4.31330.18151760.13652835X-RAY DIFFRACTION99
4.3133-5.43240.18581330.15252843X-RAY DIFFRACTION99
5.4324-42.33770.17291540.17942807X-RAY DIFFRACTION98

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