Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 97.75 kDa 
• Atom Count: 7313 
• Modelled Residue Count: 842 
• Deposited Residue Count: 846 
• Unique protein chains: 3

3FDS

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

• PDB DOI: 10.2210/pdb3FDS/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-11-26 Released: 2009-01-20 
• Deposition Author(s): Ling, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Literature

Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

Xing, G., Kirouac, K., Shin, Y.J., Bell, S.D., Ling, H.

(2009) Mol Microbiol 71: 678-691

• PubMed: 19054331 
• DOI: 10.1111/j.1365-2958.2008.06553.x
• Primary Citation of Related Structures:  
  3FDS


• PubMed Abstract: 
  

DNA polymerases are co-ordinated by sliding clamps (PCNA/beta-clamp) in translesion synthesis. It is unclear how these enzymes assemble on PCNA with geometric and functional compatibility. We report the crystal structure of a full-length Y-family polymerase, Dpo4, in complex with heterodimeric PCNA1-PCNA2 at 2.05 A resolution. Dpo4 exhibits an extended conformation that differs from the Dpo4 structures in apo- or DNA-bound form. Two hinges have been identified in Dpo4, which render the multidomain polymerase flexible conformations and orientations relative to PCNA. Dpo4 binds specifically to PCNA1 on the conserved ligand binding site. The C-terminal peptide of Dpo4 becomes structured with a 3(10) helix and dominates the specific binding. The Y-family polymerase also contacts PCNA1 with its finger, thumb and little finger domains, which are conformation-dependent protein-protein interactions that diversify the binding mode of Dpo4 on PCNA. The structure reveals a molecular model in which substrate/partner binding-coupled multiple conformations of a Y-family polymerase facilitate its recruitment and co-ordination on the sliding clamp. The conformational flexibility would turn the error-prone Y-family polymerase off when more efficient high-fidelity DNA polymerases work on undamaged DNA and turn it onto DNA templates to perform translesion synthesis when replication forks are stalled by DNA lesions.

---

Organizational Affiliation: 

Department of Biochemistry, University of Western Ontario, London, Ontario, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	A	352	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: dbh, dpo4, SSO2448 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02  Go to UniProtKB:  Q97W02

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp B	B [auth C]	249	Saccharolobus solfataricus	Mutation(s): 1  Gene Names: pcnB, pcnA-2, SSO0397, C41_008
UniProt
Find proteins for P57766 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P57766  Go to UniProtKB:  P57766

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp C	C [auth D]	245	Saccharolobus solfataricus	Mutation(s): 0  Gene Names: pcnC, pcnA-2, SSO1047
UniProt
Find proteins for Q97Z84 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Z84  Go to UniProtKB:  Q97Z84

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	U [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	JA [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	FA [auth C], T [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	GA [auth C], HA [auth C], V [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth C], BA [auth C], CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], W [auth C], X [auth C], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.240 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.986	α = 90
b = 86.414	β = 107.3
c = 97.582	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-11-26 
• Released Date: 2009-01-20 
Deposition Author(s): Ling, H.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Advisory, Refinement description
• Version 1.3: 2021-10-20
  Changes: Advisory, Database references, Derived calculations