Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 226.46 kDa 
• Atom Count: 16031 
• Modelled Residue Count: 1949 
• Deposited Residue Count: 1962 
• Unique protein chains: 1

1IQP

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

• DOI: 10.2210/pdb1IQP/pdb

• Classification: REPLICATION
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-07-24 Released: 2001-09-19 
• Deposition Author(s): Oyama, T., Ishino, Y., Cann, I.K.O., Ishino, S., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 

Literature

Atomic Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

Oyama, T., Ishino, Y., Cann, I.K.O., Ishino, S., Morikawa, K.

(2001) Mol Cell 8: 455-463

• PubMed: 11545747 
• DOI: 10.1016/s1097-2765(01)00328-8
• Primary Citation of Related Structures:  
  1IQP


• PubMed Abstract: 
  

In eukaryotic DNA replication, replication factor-C (RFC) acts as the clamp loader, which correctly installs the sliding clamp onto DNA strands at replication forks. The eukaryotic RFC is a complex consisting of one large and four small subunits. We have determined the crystal structure of the clamp loader small subunit (RFCS) from Pyrococcus furiosus. The six subunits, of which four bind ADP in their canonical nucleotide binding clefts, assemble into a dimer of semicircular trimers. The crescent-like architecture of each subunit formed by the three domains resembles that of the delta' subunit of the E. coli clamp loader. The trimeric architecture of archaeal RFCS, with its mobile N-terminal domains, involves intersubunit interactions that may be conserved in eukaryotic functional complexes.

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Related Citations: 

• Biochemical analysis of replication factor C from the hyperthermophilic archaeon Pyrococcus furiosus
  Cann, I.K.O., Ishino, S., Yuasa, M., Daiyasu, H., Toh, H., Ishino, Y.
  (2001) J Bacteriol 183: 2614

• Three-dimensional electron microscopy of the clamp loader small subunit from Pyrococcus furiosus
  Mayanagi, K., Miyata, T., Oyama, T., Ishino, Y., Morikawa, K.
  () To be published --: --

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Organizational Affiliation: 

Department of Structural Biology and, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita-City, 565-0874, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RFCS	A, B, C, D, E, F	327	Pyrococcus furiosus	Mutation(s): 0  Gene Names: rfcS
Find proteins for Q8U4J3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U4J3  Go to UniProtKB:  Q8U4J3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	G [auth A], H [auth B], I [auth C], J [auth E]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.277 
• R-Value Work: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.361	α = 90
b = 105.608	β = 90
c = 316.898	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-24 
• Released Date: 2001-09-19 
Deposition Author(s): Oyama, T., Ishino, Y., Cann, I.K.O., Ishino, S., Morikawa, K.

Revision History  

• Version 1.0: 2001-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance