5F4H | pdb_00005f4h

Archael RuvB-like Holiday junction helicase

• PDB DOI: https://doi.org/10.2210/pdb5F4H/pdb

• Classification: HYDROLASE
• Organism(s): Saccharolobus islandicus L.S.2.15
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-12-03 Released: 2016-12-21 
• Deposition Author(s): Zhai, B., DuPrez, K.T., Doukov, T.I., Shen, Y., Fan, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structure and Function of a Novel ATPase that Interacts with Holliday Junction Resolvase Hjc and Promotes Branch Migration.

Zhai, B., DuPrez, K., Doukov, T.I., Li, H., Huang, M., Shang, G., Ni, J., Gu, L., Shen, Y., Fan, L.

(2017) J Mol Biology 429: 1009-1029

• PubMed: 28238763 
• DOI: https://doi.org/10.1016/j.jmb.2017.02.016
• Primary Citation Related Structures: 
  5F4H


• PubMed Abstract: 
  

  Holliday junction (HJ) is a hallmark intermediate in DNA recombination and must be processed by dissolution (for double HJ) or resolution to ensure genome stability. Although HJ resolvases have been identified in all domains of life, there is a long-standing effort to search in prokaryotes and eukarya for proteins promoting HJ migration. Here, we report the structural and functional characterization of a novel ATPase, Sulfolobus islandicusPilT N-terminal-domain-containing ATPase (SisPINA), encoded by the gene adjacent to the resolvase Hjc coding gene. PINA is conserved in archaea and vital for S. islandicus viability. Purified SisPINA forms hexameric rings in the crystalline state and in solution, similar to the HJ migration helicase RuvB in Gram-negative bacteria. Structural analysis suggests that ATP binding and hydrolysis cause conformational changes in SisPINA to drive branch migration. Further studies reveal that SisPINA interacts with SisHjc and coordinates HJ migration and cleavage.

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Organizational Affiliation: 
• State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Road, Jinan 250100, PR China.
Department of Biochemistry, University of California, Riverside, CA 92521, USA.
Macromolecular Crystallography Group, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94309, USA.
State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nan Road, Jinan 250100, PR China. Electronic address: [e-mail].
Department of Biochemistry, University of California, Riverside, CA 92521, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (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: 346.03 kDa 
• Atom Count: 20,358 
• Modeled Residue Count: 2,616 
• Deposited Residue Count: 3,030 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide binding protein PINc	A, B, C, D, E, F	505	Saccharolobus islandicus L.S.2.15	Mutation(s): 1  Gene Names: LS215_1665 EC: 3.6.4
UniProt
Find proteins for F0NID4 (Saccharolobus islandicus (strain REY15A)) Explore F0NID4  Go to UniProtKB:  F0NID4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	BA [auth E], CA [auth E], DA [auth E], EA [auth E], FA [auth E], G [auth A], GA [auth F], H [auth A], HA [auth F], I [auth A], IA [auth F], JA [auth F], L [auth B], M [auth B], R [auth C], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Y [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth D], J [auth A], K [auth A], KA [auth F], LA [auth F], N [auth B], O [auth B], P [auth B], Q [auth B], S [auth C], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.72	α = 90
b = 148.98	β = 104.07
c = 122.13	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Zhai, B., DuPrez, K.T., Doukov, T.I., Shen, Y., Fan, L.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2017-11-01
  Changes: Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Refinement description, Structure summary