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- PDB-9qrl: DNA polymerase with inhibitor #2 -

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Basic information

Entry
Database: PDB / ID: 9qrl
TitleDNA polymerase with inhibitor #2
Components
  • DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*AP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*TP*GP*CP*GP*CP*AP*T)-3')
  • DNA (5'-D(P*TP*AP*A)-3')
  • DNA polymerase III PolC-type
KeywordsDNA BINDING PROTEIN / DNA polymerase / inhibitor complex
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA polymerase III PolC-like, N-terminal domain II / DNA polymerase III PolC-type, N-terminal domain I / DNA polymerase III polC-type N-terminus II / DNA polymerase III polC-type N-terminus I / DNA polymerase III, alpha subunit, Gram-positive type / PolC, middle finger subdomain superfamily / DNA polymerase III epsilon subunit, exonuclease domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif ...DNA polymerase III PolC-like, N-terminal domain II / DNA polymerase III PolC-type, N-terminal domain I / DNA polymerase III polC-type N-terminus II / DNA polymerase III polC-type N-terminus I / DNA polymerase III, alpha subunit, Gram-positive type / PolC, middle finger subdomain superfamily / DNA polymerase III epsilon subunit, exonuclease domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA polymerase III PolC-type
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLamers, M.H. / Urem, M. / Smits, W.K.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other governmentPOLSTOP2 Netherlands
CitationJournal: To Be Published
Title: DNA polymerase with inhibitor
Authors: Lamers, M.H. / Urem, M. / Smits, W.K.
History
DepositionApr 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III PolC-type
E: DNA (5'-D(P*TP*AP*A)-3')
P: DNA (5'-D(P*GP*GP*TP*GP*CP*GP*CP*AP*T)-3')
T: DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,11911
Polymers190,3854
Non-polymers7347
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase III PolC-type / PolIII


Mass: 166595.766 Da / Num. of mol.: 1 / Mutation: D431A, E433A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: polC, M3X98_02600 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A9X4B319, DNA-directed DNA polymerase

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DNA chain , 3 types, 3 molecules EPT

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


Mass: 885.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*GP*GP*TP*GP*CP*GP*CP*AP*T)-3')


Mass: 10179.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*AP*CP*C)-3')


Mass: 12724.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 8 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-A1I9T / 2-[(3,4-dichlorophenyl)methylamino]-7-(2-morpholin-4-ylethyl)-1~{H}-purin-6-one


Mass: 423.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20Cl2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DNA polymerase with DNA and inhibitor / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.166 MDa / Experimental value: YES
Source (natural)Organism: Enterococcus faecium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 50 mM HEPES pH 8.0 50 mM NaCl 7.5 mM MgCl2 2 mM DTT 0.05% Tween 20.
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 193 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.17.3model fitting
9PHENIX1.18.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330001 / Symmetry type: POINT
Atomic model buildingAccession code: A0A133CXW7 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410465
ELECTRON MICROSCOPYf_angle_d0.4614261
ELECTRON MICROSCOPYf_dihedral_angle_d14.6041599
ELECTRON MICROSCOPYf_chiral_restr0.041570
ELECTRON MICROSCOPYf_plane_restr0.0031769

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