Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49985.16 
• Atom Count: 3373 
• Residue Count: 382 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1S10

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

• DOI: 10.2210/pdb1S10/pdb
• NDB: PD0511

• Classification: TRANSFERASE/DNA
• Organism(s): Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
• Expression System: Escherichia coli


• Deposited: 2004-01-05 Released: 2004-03-30 
• Deposition Author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 

Literature

Snapshots of Replication through an Abasic Lesion; Structural Basis for Base Substitutions and Frameshifts.

Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

(2004) Mol.Cell 13: 751-762

• PubMed: 15023344 
• Primary Citation of Related Structures:  
  1S0O, 1S0N


• PubMed Abstract: 
  

Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase IV	A	352	Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)	Mutation(s): 0  Gene Names: dbh (dpo4) EC: 2.7.7.7
Find proteins for Q97W02 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Go to UniProtKB:  Q97W02

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'	B	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*TP*CP*AP*GP*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'	C	17	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DCP	A	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 98.395	α = 90.00
b = 102.664	β = 90.00
c = 52.340	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-05 
• Released Date: 2004-03-30 
• Deposition Author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

Revision History 

• Version 1.0: 2004-03-30
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Source and taxonomy, Version format compliance
• Version 1.3: 2018-04-04
  Type: Data collection