6AIG | pdb_00006aig

Crystal structure of PCNA1 from Aeropyrum pernix

• PDB DOI: https://doi.org/10.2210/pdb6AIG/pdb

• Classification: REPLICATION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-08-23 Released: 2018-09-26 
• Deposition Author(s): Yamauchi, T., Kikuchi, M., Tsunoda, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of proliferating cell nuclear antigen 1 from Aeropyrum pernix.

Yamauchi, T., Kikuchi, M., Iizuka, Y., Tsunoda, M.

(2024) Acta Crystallogr F Struct Biol Commun 80: 294-301

• PubMed: 39382846 
• DOI: https://doi.org/10.1107/S2053230X24009518
• Primary Citation Related Structures: 
  6AIG


• PubMed Abstract: 
  

  Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.

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Organizational Affiliation: 
• Graduate School of Life Science and Technology, Iryo Sosei University, Iwaki, Fukushima, Japan.
Graduate School of Science and Engineering, Iryo Sosei University, Iwaki, Fukushima, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.48 kDa 
• Atom Count: 2,049 
• Modeled Residue Count: 258 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase sliding clamp 1	A	263	Aeropyrum pernix K1	Mutation(s): 0  Gene Names: APE_0162
UniProt
Find proteins for Q9YFT8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YFT8  Go to UniProtKB:  Q9YFT8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.028	α = 90
b = 69.028	β = 90
c = 120.857	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Yamauchi, T., Kikuchi, M., Tsunoda, M.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2023-06-28
  Changes: Database references, Refinement description
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Database references, Structure summary