4HK1 | pdb_00004hk1

Crystal Structure of PCNA from Drosophila melanogaster

• PDB DOI: https://doi.org/10.2210/pdb4HK1/pdb

• Classification: CELL CYCLE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-14 Released: 2013-04-10 
• Deposition Author(s): Wang, K., Shi, Z.B., Zhou, Z.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: experimental

Literature

Structure of PCNA from Drosophila melanogaster.

Wang, K., Shi, Z., Zhang, M., Cheng, D.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 387-392

• PubMed: 23545643 
• DOI: https://doi.org/10.1107/S1744309113004971
• Primary Citation Related Structures: 
  4HK1


• PubMed Abstract: 
  

  Proliferating cell nuclear antigen (PCNA) plays essential roles in DNA replication, DNA repair, cell-cycle regulation and chromatin metabolism. The PCNA from Drosophila melanogaster (DmPCNA) was purified and crystallized. The crystal of DmPCNA diffracted to 2.0 Å resolution and belonged to space group H3, with unit-cell parameters a = b = 151.16, c = 38.28 Å. The structure of DmPCNA was determined by molecular replacement. DmPCNA forms a symmetric homotrimer in a head-to-tail manner. An interdomain connector loop (IDCL) links the N- and C-terminal domains. Additionally, the N-terminal and C-terminal domains contact each other through hydrophobic associations. Compared with human PCNA, the IDCL of DmPCNA has conformational changes, which may explain their difference in function. This work provides a structural basis for further functional and evolutionary studies of PCNA.

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Organizational Affiliation: 
• Department of Biology, Qingdao University, Qingdao, Shandong 266021, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.13 kDa 
• Atom Count: 1,960 
• Modeled Residue Count: 243 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A	263	Drosophila melanogaster	Mutation(s): 0  Gene Names: mus209, PCNA, CG9193
UniProt
Find proteins for P17917 (Drosophila melanogaster) Explore P17917  Go to UniProtKB:  P17917

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.278 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.157	α = 90
b = 151.157	β = 90
c = 38.282	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Wang, K., Shi, Z.B., Zhou, Z.C.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description