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

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Basic information

Entry
Database: PDB / ID: 9cih
TitleCrystal structure of human polymerase eta with incoming dCMPnPP nucleotide across O4-methyl 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*(A1A0L)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: 2.15 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 3, 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*(A1A0L)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)55,4989
Polymers54,7073
Non-polymers7916
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-36 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.470, 98.470, 81.900
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: 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 (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*(A1A0L)P*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3653.390 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: DNA template strand containing modified nucleotide, O4-methyl threofuranosyl thymidine
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, 321 molecules

#4: 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
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 41.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 5mM magnesium chloride, 22% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 24623 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 21.5 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.045 / Rsym value: 0.104 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1809 / CC1/2: 0.768 / Rpim(I) all: 0.319 / Rsym value: 0.737 / % 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: 2.15→42.2 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1291 5.25 %
Rwork0.1701 --
obs0.1734 24591 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 389 48 315 4075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.937
X-RAY DIFFRACTIONf_dihedral_angle_d20.571682
X-RAY DIFFRACTIONf_chiral_restr0.051591
X-RAY DIFFRACTIONf_plane_restr0.009617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.26661430.20522555X-RAY DIFFRACTION100
2.24-2.340.2771750.19792555X-RAY DIFFRACTION100
2.34-2.460.26011250.20222606X-RAY DIFFRACTION100
2.46-2.620.2441140.20132580X-RAY DIFFRACTION100
2.62-2.820.31281270.19162619X-RAY DIFFRACTION100
2.82-3.10.27261500.18492574X-RAY DIFFRACTION100
3.1-3.550.26281630.1582577X-RAY DIFFRACTION100
3.55-4.470.15971520.1362598X-RAY DIFFRACTION100
4.47-42.20.19321420.15272636X-RAY DIFFRACTION100

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