› 3rb6

X-ray diffraction
2.7Å resolution

Dpo4 extension ternary complex with 3'-terminal primer A base opposite the 3-methylcytosine (m3c) lesion

Released:
DOI: 10.2210/pdb3rb6/pdb
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PDB entry 3rb6 coloured by chain, front view.
PDB entry 3rb6 coloured by chain, side view.
PDB entry 3rb6 coloured by chain, top view.
Source organism: Saccharolobus solfataricus P2
Primary publication:
Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.
Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ
Structure 19 821-32 (2011)
PMID: 21645853

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116807 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase IV Chains: A, B
Molecule details ›
Chains: A, B
Length: 341 amino acids
Theoretical weight: 38.95 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q97W02 (Residues: 2-341; Coverage: 97%)
Gene names: SSO2448, dbh, dpo4
Sequence domains:
Structure domains:
DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DA))-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Saccharolobus solfataricus P2
Expression system: Not provided
DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3') Chains: E, J

Ligands and Environments

3 bound ligands:
Ligand DGT 2 x DGT
Ligand EPE 1 x EPE
Ligand CA 6 x CA
2 modified residues:
Ligand 2DA 2 x 2DA
Ligand ME6 2 x ME6

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 52.915Å b: 109.328Å c: 100.828Å
α: 90° β: 101.07° γ: 90°
R-values:
R R work R free
0.205 0.203 0.247
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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Citations

4 citation in other articles

Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation.
Carvalho et al. (2014)
3 more

2 mentions without citation

3dDNA: A Computational Method of Building DNA 3D Structures.
Zhang et al. (2022)
1 more

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