3MXZ | pdb_00003mxz

Crystal Structure of tubulin folding cofactor A from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb3MXZ/pdb

• Classification: CHAPERONE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-08 Released: 2010-09-01 
• Deposition Author(s): Lu, L., Nan, J., Mi, W., Su, X.D., Li, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.208 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of tubulin folding cofactor A from Arabidopsis thaliana and its beta-tubulin binding characterization

Lu, L., Nan, J., Mi, W., Li, L.F., Wei, C.H., Su, X.D., Li, Y.

(2010) FEBS Lett 584: 3533-3539

• PubMed: 20638386 
• DOI: https://doi.org/10.1016/j.febslet.2010.07.017
• Primary Citation Related Structures: 
  3MXZ


• PubMed Abstract: 
  

  Microtubules are composed of polymerized alpha/beta-tubulin heterodimers. Biogenesis of assembly-competent tubulin dimers is a complex multistep process that requires sequential actions of distinct molecular chaperones and cofactors. Tubulin folding cofactor A (TFCA), which captures beta-tubulin during the folding pathway, has been identified in many organisms. Here, we report the crystal structure of Arabidopsis thaliana TFC A (KIESEL, KIS), which forms a monomeric three-helix bundle. The functional binding analysis demonstrated that KIS interacts with beta-tubulin in plant. Furthermore, mutagenesis studies indicated that the alpha-helical regions of KIS participate in beta-tubulin binding. Unlike the budding yeast TFC A, the two loop regions of KIS are not required for this interaction suggesting a distinct binding mechanism of TFC A to beta-tubulin in plants.

---

Organizational Affiliation: 
• The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China.

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: 13.25 kDa 
• Atom Count: 1,008 
• Modeled Residue Count: 107 
• Deposited Residue Count: 116 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin-specific chaperone A	A	116	Arabidopsis thaliana	Mutation(s): 0  Gene Names: KIS
UniProt
Find proteins for O04350 (Arabidopsis thaliana) Explore O04350  Go to UniProtKB:  O04350

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	B [auth A], C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.208 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.974	α = 90
b = 54.974	β = 90
c = 67.419	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-01 
Deposition Author(s): Lu, L., Nan, J., Mi, W., Su, X.D., Li, Y.

Revision History  

• Version 1.0: 2010-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description