5BQ5 | pdb_00005bq5

Crystal structure of the IstB AAA+ domain bound to ADP-BeF3

• PDB DOI: https://doi.org/10.2210/pdb5BQ5/pdb

• Classification: ATP-binding protein
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-28 Released: 2015-09-02 
• Deposition Author(s): Arias-Palomo, E., Berger, J.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

An Atypical AAA+ ATPase Assembly Controls Efficient Transposition through DNA Remodeling and Transposase Recruitment.

Arias-Palomo, E., Berger, J.M.

(2015) Cell 162: 860-871

• PubMed: 26276634 
• DOI: https://doi.org/10.1016/j.cell.2015.07.037
• Primary Citation Related Structures: 
  5BQ5


• PubMed Abstract: 
  

  Transposons are ubiquitous genetic elements that drive genome rearrangements, evolution, and the spread of infectious disease and drug-resistance. Many transposons, such as Mu, Tn7, and IS21, require regulatory AAA+ ATPases for function. We use X-ray crystallography and cryo-electron microscopy to show that the ATPase subunit of IS21, IstB, assembles into a clamshell-shaped decamer that sandwiches DNA between two helical pentamers of ATP-associated AAA+ domains, sharply bending the duplex into a 180° U-turn. Biochemical studies corroborate key features of the structure and further show that the IS21 transposase, IstA, recognizes the IstB•DNA complex and promotes its disassembly by stimulating ATP hydrolysis. Collectively, these studies reveal a distinct manner of higher-order assembly and client engagement by a AAA+ ATPase and suggest a mechanistic model where IstB binding and subsequent DNA bending primes a selected insertion site for efficient transposition.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 67.46 kDa 
• Atom Count: 5,094 
• Modeled Residue Count: 547 
• Deposited Residue Count: 567 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insertion sequence IS5376 putative ATP-binding protein	A, B, C	189	Geobacillus stearothermophilus	Mutation(s): 0
UniProt
Find proteins for Q45619 (Geobacillus stearothermophilus) Explore Q45619  Go to UniProtKB:  Q45619

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], G [auth B], J [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF	F [auth A], I [auth B], L [auth C]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	E [auth A], H [auth B], K [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.203 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.806	α = 90
b = 133.806	β = 90
c = 70.95	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Arias-Palomo, E., Berger, J.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM071747

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary