Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.34 kDa 
• Atom Count: 2269 
• Modelled Residue Count: 289 
• Deposited Residue Count: 303 
• Unique protein chains: 1

6QV5

Crystal structure of the CHAD domain from the plant Ricinus communis

• PDB DOI: 10.2210/pdb6QV5/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Ricinus communis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-03-01 Released: 2019-05-29 
• Deposition Author(s): Lorenzo-Orts, L., Hothorn, M.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

Literature

Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules.

Lorenzo-Orts, L., Hohmann, U., Zhu, J., Hothorn, M.

(2019) Life Sci Alliance 2

• PubMed: 31133615 
• DOI: 10.26508/lsa.201900385
• Primary Citation of Related Structures:  
  6QV5, 6QV7, 6QVA


• PubMed Abstract: 
  

Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Here, we report that bacterial, archaeal, and eukaryotic conserved histidine α-helical (CHAD) domains are specific polyP-binding modules. Crystal structures reveal that CHAD domains are formed by two four-helix bundles, giving rise to a central pore surrounded by conserved basic surface patches. Different CHAD domains bind polyPs with dissociation constants ranging from the nano- to mid-micromolar range, but not nucleic acids. A CHAD-polyP complex structure reveals the phosphate polymer binding across the central pore and along the two basic patches. Mutational analysis of CHAD-polyP interface residues validates the complex structure. The presence of a CHAD domain in the polyPase ygiF enhances its enzymatic activity. The only known CHAD protein from the plant Ricinus communis localizes to the nucleus/nucleolus when expressed in Arabidopsis and tobacco, suggesting that plants may harbor polyPs in these compartments. We propose that CHAD domains may be used to engineer the properties of polyP-metabolizing enzymes and to specifically localize polyP stores in eukaryotic cells and tissues.

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Organizational Affiliation: 

Structural Plant Biology Laboratory, Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAD domain	A	303	Ricinus communis	Mutation(s): 0  Gene Names: RCOM_0386350
UniProt
Find proteins for B9T8Q5 (Ricinus communis) Explore B9T8Q5  Go to UniProtKB:  B9T8Q5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.242 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.427	α = 90
b = 116.427	β = 90
c = 119.248	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-01 
• Released Date: 2019-05-29 
Deposition Author(s): Lorenzo-Orts, L., Hothorn, M.

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Funding Organization	Location	Grant Number
European Research Council	Switzerland	310856

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-06-05
  Changes: Data collection, Database references