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- PDB-6h1v: The crystal structure of Pol2CORE in complex with DNA and an inco... -

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Basic information

Entry
Database: PDB / ID: 6h1v
TitleThe crystal structure of Pol2CORE in complex with DNA and an incoming nucleotide, carrying an Fe-S cluster
Components
  • DNA (5'-D(P*AP*AP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3')
  • DNA polymerase epsilon catalytic subunit A
KeywordsDNA BINDING PROTEIN / Pol epsilon / M644G / DNA / complex / Fe-S
Function / homology
Function and homology information


gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / nucleotide-excision repair, DNA gap filling / SUMO binding / DNA replication proofreading / Activation of the pre-replicative complex / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / leading strand elongation / nuclear replication fork / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / double-strand break repair / single-stranded DNA binding / mitotic cell cycle / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / mRNA binding / DNA binding / zinc ion binding / nucleus
Similarity search - Function
DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily ...DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / IRON/SULFUR CLUSTER / DNA / DNA (> 10) / DNA polymerase epsilon catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsParkash, V. / Johansson, E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural evidence for an essential Fe-S cluster in the catalytic core domain of DNA polymerase ε.
Authors: Ter Beek, J. / Parkash, V. / Bylund, G.O. / Osterman, P. / Sauer-Eriksson, A.E. / Johansson, E.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase epsilon catalytic subunit A
P: DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3')
T: DNA (5'-D(P*AP*AP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7886
Polymers144,9213
Non-polymers8673
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-48 kcal/mol
Surface area50880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.210, 70.040, 149.930
Angle α, β, γ (deg.)90.000, 109.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase epsilon catalytic subunit A / DNA polymerase II subunit A


Mass: 136738.297 Da / Num. of mol.: 1 / Mutation: D290A and E292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: POL2, DUN2, YNL262W, N0825 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21951, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*(DOC))-3')


Mass: 3293.174 Da / Num. of mol.: 1 / Mutation: Di-Deoxycytosine / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*AP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')


Mass: 4889.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 9 molecules

#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.5351.35
22.5351.35
Crystal grow
Temperature (K)Crystal-IDMethodpHDetailsPH range
2911vapor diffusion, hanging drop720% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)7-7.5
2912vapor diffusion, hanging drop720% PEG-3350, 50 mM Hepes-NaOH pH 7.0, 10 mM MgCl2, 400 mM LiAc, and 10 mM 2-aminoethanesulfonic acid (taurine)7-7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.984
SYNCHROTRONESRF ID23-121.73598
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJul 13, 2017
DECTRIS PILATUS3 6M2PIXELNov 5, 2017
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
21.735981
Reflection

Entry-ID: 6H1V

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
2.7-73.043954398.62.957.090.9720.1520.1060.18615.1
6-20674894.91.820.033224.03
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.7 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.811.65443950.1441.1882.04697.5
9.74-73.040.0599020.9450.0430.07398.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m8o

4m8o


Resolution: 2.7→19.99 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2659 1956 4.98 %
Rwork0.2386 37294 -
obs0.24 39250 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.85 Å2 / Biso mean: 64.9752 Å2 / Biso min: 12.79 Å2
Refinement stepCycle: final / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8428 529 39 6 9002
Biso mean--38.6 38.59 -
Num. residues----1138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.76740.39621200.36572560268095
2.7674-2.8420.38741320.37122601273395
2.842-2.92540.36141660.34592666283299
2.9254-3.01950.33731460.33222654280099
3.0195-3.12710.33021380.31282659279799
3.1271-3.25180.35331320.30122661279399
3.2518-3.39910.32451450.29162628277398
3.3991-3.57730.26261480.25312652280097
3.5773-3.80.25561420.23722653279599
3.8-4.09110.281320.22762724285699
4.0911-4.49860.21251270.2032656278398
4.4986-5.13980.2281310.1932750288199
5.1398-6.43950.25841340.21412700283498
6.4395-19.99090.20031630.17312730289398

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