5A2H

Crystal Structure of Arabidopsis thaliana Calmodulin-7

• PDB DOI: https://doi.org/10.2210/pdb5A2H/pdb

• Classification: CALCIUM-BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-19 Released: 2016-03-30 
• Deposition Author(s): Kumar, S., Gourinath, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Crystal Structure of Arabidopsis Thaliana Calmodulin7 and Insight Into its Mode of DNA Binding.

Kumar, S., Mazumder, M., Gupta, N., Chattopadhyay, S., Gourinath, S.

(2016) FEBS Lett 590: 3029

• PubMed: 27500568 
• DOI: https://doi.org/10.1002/1873-3468.12349
• Primary Citation of Related Structures:  
  5A2H


• PubMed Abstract: 
  

  Calmodulin (CaM) is a Ca(2+) sensor that participates in several cellular signaling cascades by interacting with various targets, including DNA. It has been shown that Arabidopsis thaliana CaM7 (AtCaM7) interacts with Z-box DNA and functions as a transcription factor [Kushwaha R et al. (2008) Plant Cell 20, 1747-1759; Abbas N et al. (2014) Plant Cell 26, 1036-1052]. The crystal structure of AtCaM7, and a model of the AtCAM7-Z-box complex suggest that Arg-127 determines the DNA-binding ability by forming crucial interactions with the guanine base. We validated the model using biolayer interferometry, which confirmed that AtCaM7 interacts with Z-box DNA with high affinity. In contrast, the AtCaM2/3/5 isoform does not show any binding, although it differs from AtCaM7 by only a single residue.

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Organizational Affiliation: 

School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 17.44 kDa 
• Atom Count: 1,235 
• Modelled Residue Count: 147 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CALMODULIN	A	149	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59220 (Arabidopsis thaliana) Explore P59220  Go to UniProtKB:  P59220

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth A], G [auth A], H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.455	α = 90
b = 67.901	β = 90
c = 111.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Kumar, S., Gourinath, S.

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2016-09-28
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description