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- PDB-4q8e: Human DNA polymerase eta inserting dCMPNPP opposite a phenanthrip... -

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Basic information

Entry
Database: PDB / ID: 4q8e
TitleHuman DNA polymerase eta inserting dCMPNPP opposite a phenanthriplatin adducted G
Components
  • 5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'
  • 5'-D(*CP*AP*TP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / metal ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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 ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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 polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsGregory, M.T. / Yang, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and mechanistic studies of polymerase eta bypass of phenanthriplatin DNA damage.
Authors: Gregory, M.T. / Park, G.Y. / Johnstone, T.C. / Lee, Y.S. / Yang, W. / Lippard, S.J.
History
DepositionApr 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Jun 27, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _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
A: DNA polymerase eta
T: 5'-D(*CP*AP*TP*GP*CP*TP*CP*AP*CP*AP*CP*T)-3'
P: 5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3029
Polymers54,5113
Non-polymers7916
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-42 kcal/mol
Surface area22030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.766, 98.766, 82.197
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, POLH RAD30 RAD30A XPV, RAD30, RAD30A, XPV / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 3386.309 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthesized by Sigma-Aldrich and adducted with phenanthriplatin
#3: DNA chain 5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3'


Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by Sigma-Aldrich

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Non-polymers , 4 types, 400 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 2000-MME, MES, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.549→30 Å / Num. obs: 65955 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.078 / Χ2: 1.007 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.583.20.6632591.006199.5
1.58-1.613.20.58532831.027199.5
1.61-1.643.20.53132591.023199.6
1.64-1.673.30.43833140.907199.7
1.67-1.713.30.39432651.001199.8
1.71-1.753.30.33832980.991199.8
1.75-1.793.40.29132930.972199.8
1.79-1.843.40.24932960.967199.9
1.84-1.893.40.2132821.028199.9
1.89-1.953.40.17233041.024199.9
1.95-2.023.40.1332941.001199.9
2.02-2.13.40.11133041.0351100
2.1-2.23.40.09932881.0791100
2.2-2.323.40.09933050.9581100
2.32-2.463.40.10333131.0331100
2.46-2.653.40.10232961.0691100
2.65-2.923.40.0833301.0631100
2.92-3.343.40.0633131.0111100
3.34-4.23.40.04133300.971199.9
4.2-303.30.03633290.969197.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.14data extraction
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.549→26.937 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 5122 7.77 %Copied from 3MR2 and extended randomly.
Rwork0.1832 ---
obs0.1864 65893 99.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.87 Å2 / Biso mean: 21.9214 Å2 / Biso min: 4.39 Å2
Refinement stepCycle: LAST / Resolution: 1.549→26.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 380 48 394 4180

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