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- PDB-6g0a: The crystal structure of the Pol2 catalytic domain of DNA polymer... -

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Basic information

Entry
Database: PDB / ID: 6g0a
TitleThe crystal structure of the Pol2 catalytic domain of DNA polymerase epsilon carrying a P301R substitution.
Components
  • DNA (5'-D(P*TP*AP*AP*CP*CP*GP*CP*GP*TP*TP*DC)-3')
  • DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')
  • DNA polymerase epsilon catalytic subunit A
KeywordsDNA BINDING PROTEIN / DNA / Pol2 / PolE / Epsilon / P301R / cancer
Function / homology
Function and homology information


gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / DNA replication proofreading / Termination of translesion DNA synthesis / single-stranded DNA 3'-5' DNA exonuclease activity / mitotic DNA replication checkpoint signaling ...gene conversion / DNA replication initiation / epsilon DNA polymerase complex / SUMO binding / nucleotide-excision repair, DNA gap filling / Activation of the pre-replicative complex / DNA replication proofreading / Termination of translesion DNA synthesis / 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 / Dual incision in TC-NER / error-prone translesion synthesis / base-excision repair, gap-filling / replication fork / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / double-strand break repair / mitotic cell cycle / single-stranded DNA binding / 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, thumb domain / Zinc finger domain of DNA polymerase-epsilon / 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 epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / 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 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 / : / 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: 2.62 Å
AuthorsParkash, V. / Johansson, E.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Cancerfonden Sweden
Knut and Alice Wallenberg Foundation2011.0042 Sweden
CitationJournal: Nat Commun / Year: 2019
Title: Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase epsilon.
Authors: Parkash, V. / Kulkarni, Y. / Ter Beek, J. / Shcherbakova, P.V. / Kamerlin, S.C.L. / Johansson, E.
History
DepositionMar 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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*DC)-3')
T: DNA (5'-D(P*TP*CP*TP*TP*GP*AP*AP*CP*GP*CP*GP*GP*TP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7567
Polymers145,1293
Non-polymers6274
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-53 kcal/mol
Surface area49370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.895, 67.252, 151.639
Angle α, β, γ (deg.)90.000, 111.500, 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: 137235.672 Da / Num. of mol.: 1 / Mutation: P301R
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: Escherichia coli BL21(DE3) (bacteria) / 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*DC)-3')


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


Mass: 4599.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 19 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50mM MES pH 6.5, 150mM NaAc and 8% PEG20K / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2017
RadiationMonochromator: Si (111) Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.62→78.78 Å / Num. obs: 44773 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 48.1 Å2 / CC1/2: 0.829 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.087 / Rrim(I) all: 0.156 / Net I/σ(I): 5.9 / Num. measured all: 136067 / Scaling rejects: 76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.62-2.712.80.8591230243510.3680.6011.0541.398.2
10.15-78.782.90.08624118300.6530.0680.1118.197.8

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Processing

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

4m8o


Resolution: 2.62→19.977 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 2289 5.13 %
Rwork0.224 42336 -
obs0.226 44625 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.3 Å2 / Biso mean: 53.9482 Å2 / Biso min: 20.86 Å2
Refinement stepCycle: final / Resolution: 2.62→19.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8625 529 33 15 9202
Biso mean--33.06 42.52 -
Num. residues----1129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.62-2.67680.41381590.38532593275298
2.6768-2.7390.40421400.3672560270097
2.739-2.80730.36891400.33682681282199
2.8073-2.8830.34261600.31032606276699
2.883-2.96750.3151430.29592635277899
2.9675-3.0630.30711430.28382693283699
3.063-3.1720.30971230.26992592271598
3.172-3.29850.28741400.25382636277698
3.2985-3.44790.31491480.24572602275097
3.4479-3.62870.29581340.23392651278599
3.6287-3.85450.28391400.21962663280399
3.8545-4.14960.24521340.20382691282599
4.1496-4.56270.20761460.17792605275197
4.5627-5.21270.24961460.175426972843100
5.2127-6.52920.22051500.19452668281898
6.5292-19.97780.18171430.16052763290699

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