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- PDB-7m7n: Human DNA Pol eta with 2'-FA-ended primer and dAMPNPP -

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Basic information

Entry
Database: PDB / ID: 7m7n
TitleHuman DNA Pol eta with 2'-FA-ended primer and dAMPNPP
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(AF5))-3')
  • DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA polymerase / Time resolved crystallography / deprotonation / DNA BINDING PROTEIN / 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 / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family ...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 / 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/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.31 Å
AuthorsGregory, M.T. / Gao, Y. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
Authors: Gregory, M.T. / Gao, Y. / Cui, Q. / Yang, W.
History
DepositionMar 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(AF5))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,00510
Polymers54,7003
Non-polymers1,3057
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-46 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.444, 98.444, 82.105
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and residue 505
21chain A and residue 506
31chain A and residue 507

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GOL / Beg label comp-ID: GOL / End auth comp-ID: GOL / End label comp-ID: GOL / Auth asym-ID: A

Dom-IDSelection detailsLabel asym-IDAuth seq-ID
1chain BH505
2chain DI506
3chain EJ507

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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 / Cell (production host): Escherichia coli / 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*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3628.377 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*(AF5))-3')


Mass: 2453.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 530 molecules

#4: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 41.42 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6 / Details: 15% PEG 2000 MME, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→30 Å / Num. obs: 104816 / % possible obs: 97.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.057 / Χ2: 1.025 / Net I/σ(I): 11.1 / Num. measured all: 413501
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.31-1.333.50.68949780.976192.6
1.33-1.363.80.63651411.015195.5
1.36-1.383.90.53951830.999195.9
1.38-1.413.90.48251671.011196.2
1.41-1.4440.42851731.009196.3
1.44-1.4840.33551961.012196.8
1.48-1.5140.27952041.024196.8
1.51-1.5540.22852281.036196.9
1.55-1.640.18852551.047197.5
1.6-1.6540.15952201.065197.4
1.65-1.7140.13252971.05197.7
1.71-1.7840.10752741.052197.8
1.78-1.8640.09152611.023197.8
1.86-1.9640.07452841.067197.8
1.96-2.0840.06253021.027198.1
2.08-2.2440.05652771.006197.6
2.24-2.4740.05253210.981198.3
2.47-2.8240.04753750.997199.1
2.82-3.5540.03454091.058199.4
3.55-303.90.02652711.04195.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ECQ

4ecq


Resolution: 1.31→21.31 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 8047 7.68 %
Rwork0.1843 96762 -
obs0.1863 104809 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.83 Å2 / Biso mean: 20.1733 Å2 / Biso min: 6.09 Å2
Refinement stepCycle: final / Resolution: 1.31→21.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 379 61 524 4280
Biso mean--16.28 28.08 -
Num. residues----445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064084
X-RAY DIFFRACTIONf_angle_d0.875627
X-RAY DIFFRACTIONf_dihedral_angle_d26.0181640
X-RAY DIFFRACTIONf_chiral_restr0.068631
X-RAY DIFFRACTIONf_plane_restr0.005646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6X-RAY DIFFRACTION54.698TORSIONAL
12A6X-RAY DIFFRACTION54.698TORSIONAL
13A6X-RAY DIFFRACTION54.698TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.320.29922220.28472682290481
1.32-1.340.2862580.26313123338194
1.34-1.360.27272720.26063173344596
1.36-1.370.25792720.24593196346896
1.37-1.390.23992360.2293233346996
1.39-1.410.23252490.23223221347096
1.41-1.430.25822590.23363188344796
1.43-1.450.27242600.22273235349597
1.45-1.470.24252850.22013191347697
1.48-1.50.23752630.21313211347497
1.5-1.530.24392580.2093269352797
1.53-1.550.23092580.19423202346097
1.55-1.580.21312610.19353239350097
1.58-1.610.20722870.1873232351998
1.61-1.650.21182740.1883246352098
1.65-1.690.20232610.1863272353398
1.69-1.730.19073150.18463211352698
1.73-1.780.20292630.18843259352298
1.78-1.830.23492690.19153273354298
1.83-1.890.2313030.18913236353998
1.89-1.960.19892580.18353248350698
1.96-2.030.22412670.18583290355798
2.03-2.130.19562610.18023265352698
2.13-2.240.21942920.18013235352798
2.24-2.380.21862460.18223300354698
2.38-2.560.23663210.19043268358999
2.56-2.820.21082760.18263329360599
2.82-3.230.19412590.17793342360199
3.23-4.060.1812830.148133493632100
4.06-21.310.1732590.16353244350395

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