5ZKT | pdb_00005zkt

Crystal structure of TCP domain of PCF6 in Oryza sativa

• PDB DOI: https://doi.org/10.2210/pdb5ZKT/pdb

• Classification: TRANSCRIPTION
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-03-26 Released: 2019-03-27 
• Deposition Author(s): Sun, L.F., Zou, X.M., Wu, Y.K.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

The crystal structure of the TCP domain of PCF6 in Oryza sativa L. reveals an RHH-like fold.

Sun, L., Zou, X., Jiang, M., Wu, X., Chen, Y., Wang, Q., Wang, Q., Chen, L., Wu, Y.

(2020) FEBS Lett 594: 1296-1306

• PubMed: 31898812 
• DOI: https://doi.org/10.1002/1873-3468.13727
• Primary Citation of Related Structures:  
  5ZKT


• PubMed Abstract: 
  

  The Teosinte branched 1/Cycloidea/Proliferating cell factor (TCP) domain is an evolutionarily conserved DNA binding domain unique to the plant kingdom. To date, the functions of TCPs have been well studied, but the three-dimensional structure of the TCP domain is lacking. Here, we have determined the crystal structure of the TCP domain from OsPCF6. The structure reveals that the TCP domain adopts three short β-strands followed by a helix-loop-helix structure, distinct from the canonical basic helix-loop-helix structure. This folded domain shows high structural similarity to the ribbon-helix-helix (RHH) transcriptional repressors, a family of DNA binding proteins with a conserved 3D structural motif (RHH fold), indicating that TCPs could be reclassified as RHH proteins. Our work will provide insight toward a better understanding of the mechanisms underlying TCP protein function.

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Organizational Affiliation: 
• Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.
State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.
Department of Molecular Biology, University of Geneva, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 12.44 kDa 
• Atom Count: 955 
• Modeled Residue Count: 109 
• Deposited Residue Count: 110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcription factor PCF6	A, B	55	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: B1364A02.22, OJ1048_C10.23
UniProt
Find proteins for Q0D8K4 (Oryza sativa subsp. japonica) Explore Q0D8K4  Go to UniProtKB:  Q0D8K4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.28	α = 90
b = 43.71	β = 90
c = 72.37	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Sun, L.F., Zou, X.M., Wu, Y.K.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31470741

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references
• Version 1.2: 2026-02-11
  Changes: Database references, Structure summary