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- PDB-9ci9: Crystal structure of human polymerase eta with incoming dCMPnPP n... -

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Basic information

Entry
Database: PDB / ID: 9ci9
TitleCrystal structure of human polymerase eta with incoming dCMPnPP nucleotide across threofuranosyl thymidine in DNA template at extension stage
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
  • DNA (5'-D(*CP*AP*TP*GP*(TFT)P*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA binding protein / 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-0KX / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 2, 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*GP*(TFT)P*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4849
Polymers54,6933
Non-polymers7916
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-39 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.902, 98.902, 81.540
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 eta (1-432 residues) along with additional "GPH" residues (at N-terminal )from plasmid constructs 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*GP*(TFT)P*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3639.364 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA Template strand containing threofuranosyl thymidine (TFT) as modified nucleotide with 3'-2' phosphodiester linkage
Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')


Mass: 2435.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 315 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 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MES pH 5.6, 5mM magnesium chloride, 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 26703 / % possible obs: 98.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.049 / Rsym value: 0.1 / Net I/σ(I): 19.3
Reflection shellResolution: 2.09→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.34 / Num. unique obs: 947 / CC1/2: 0.72 / Rpim(I) all: 0.287 / Rsym value: 0.494 / % possible all: 70.8

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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: 2.09→36.81 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 1279 4.8 %
Rwork0.1576 --
obs0.16 26638 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 388 48 309 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.905
X-RAY DIFFRACTIONf_dihedral_angle_d19.5561507
X-RAY DIFFRACTIONf_chiral_restr0.05594
X-RAY DIFFRACTIONf_plane_restr0.008615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.180.23461120.19412762X-RAY DIFFRACTION98
2.18-2.280.25531420.17162809X-RAY DIFFRACTION100
2.28-2.40.20171240.17692831X-RAY DIFFRACTION100
2.4-2.550.23151400.1742823X-RAY DIFFRACTION100
2.55-2.740.23051520.17812801X-RAY DIFFRACTION100
2.74-3.020.22161420.16872829X-RAY DIFFRACTION100
3.02-3.460.20281670.14552796X-RAY DIFFRACTION100
3.46-4.350.17311580.13352828X-RAY DIFFRACTION100
4.36-36.810.19871420.14932880X-RAY DIFFRACTION100

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