5KXF | pdb_00005kxf

Crystal structure of the SPOC domain of the Arabidopsis flowering regulator FPA

• PDB DOI: https://doi.org/10.2210/pdb5KXF/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-20 Released: 2016-10-12 
• Deposition Author(s): Zhang, Y., Tong, L.
• 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: 2.70 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA.

Zhang, Y., Rataj, K., Simpson, G.G., Tong, L.

(2016) PLoS One 11: e0160694-e0160694

• PubMed: 27513867 
• DOI: https://doi.org/10.1371/journal.pone.0160694
• Primary Citation Related Structures: 
  5KXF


• PubMed Abstract: 
  

  The Arabidopsis protein FPA controls flowering time by regulating the alternative 3'-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3'-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain.

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Organizational Affiliation: 
• Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America.
Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom.
Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.33 kDa 
• Atom Count: 959 
• Modeled Residue Count: 123 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flowering time control protein FPA	A	156	Arabidopsis thaliana	Mutation(s): 0  Gene Names: FPA, At2g43410, T1O24.15
UniProt
Find proteins for Q8LPQ9 (Arabidopsis thaliana) Explore Q8LPQ9  Go to UniProtKB:  Q8LPQ9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.151	α = 90
b = 108.151	β = 90
c = 34.208	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Zhang, Y., Tong, L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM077175

Revision History  

• Version 1.0: 2016-10-12
  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, Structure summary