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- PDB-9cj9: Crystal structure of human polymerase eta with incoming dAMPnPP n... -

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Basic information

Entry
Database: PDB / ID: 9cj9
TitleCrystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite O4-methyl threofuranosyl thymidine in DNA template at insertion stage
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA (5'-D(*CP*AP*TP*(TFT)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA binding / DNA polymerase / TRANSFERASE / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsTomar, R. / Stone, M.P. / Egli, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01ES029357 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)2P01CA160032-26A1 United States
CitationJournal: Biochemistry / Year: 2024
Title: DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Authors: Tomar, R. / Ghodke, P.P. / Patra, A. / Smyth, E. / Pontarelli, A. / Copp, W. / Guengerich, F.P. / Chaput, J.C. / Wilds, C.J. / Stone, M.P. / Egli, M.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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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*(TFT)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)55,2216
Polymers54,6823
Non-polymers5393
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-42 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.080, 98.080, 78.660
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
Source method: isolated from a genetically manipulated source
Details: Human polymerase (1-432 amino acid) along with "GPH" residues coming from plasmid sequence (at N-terminal) were expressed
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*(TFT)P*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA template strand containing modified nucleotide, O4-methyl threofuranosyl thymidine (A1A0L) connected through 3'-2' phosphodiester linkage through neighbor nucleotides
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 / Details: DNA primer strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 37 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.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Details: incoming non-hydrolyzable nucleotide dAMPnPP / 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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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 Å3/Da / Density % sol: 38.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 5mM magnesium chloride, 16% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 8479 / % possible obs: 95.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.059 / Rsym value: 0.133 / Net I/σ(I): 10.9
Reflection shellResolution: 2.98→3.06 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 653 / CC1/2: 0.393 / Rpim(I) all: 0.818 / Rsym value: 1.86 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v721.2data reduction
HKL-2000v721.2data scaling
PHASER1.20.1_4487phasing
Coot0.9.8.91EL (ccp4)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→41.61 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3481 386 4.56 %
Rwork0.2204 --
obs0.2265 8466 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 387 32 34 3797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.155
X-RAY DIFFRACTIONf_dihedral_angle_d24.0181513
X-RAY DIFFRACTIONf_chiral_restr0.049595
X-RAY DIFFRACTIONf_plane_restr0.01620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.410.37261110.28682722X-RAY DIFFRACTION96
3.41-4.30.39881360.20952513X-RAY DIFFRACTION90
4.3-41.610.29081390.18942845X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -48.9024 Å / Origin y: 1.5557 Å / Origin z: 3.6863 Å
111213212223313233
T0.2038 Å20.0182 Å20.0451 Å2-0.092 Å20.0058 Å2--0.0652 Å2
L1.258 °2-0.4043 °2-0.1005 °2-0.88 °20.081 °2--0.4161 °2
S0.1626 Å °-0.0648 Å °0.1061 Å °0.0238 Å °-0.0579 Å °0.0197 Å °-0.0278 Å °0.1181 Å °-0.0648 Å °
Refinement TLS groupSelection details: all

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