1IQP | pdb_00001iqp

Crystal Structure of the Clamp Loader Small Subunit from Pyrococcus furiosus

• PDB DOI: https://doi.org/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 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.221 (DCC) 

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: https://doi.org/10.1016/s1097-2765(01)00328-8
• Primary Citation 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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Organizational Affiliation: 
• Department of Structural Biology and, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita-City, 565-0874, Osaka, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
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: 16,031 
• Modeled Residue Count: 1,949 
• Deposited Residue Count: 1,962 
• Unique protein chains: 1

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
UniProt
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 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.221 (DCC) 

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

• 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
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations