5G49

Crystal structure of the Arabodopsis thaliana histone-fold dimer L1L NF-YC3

• PDB DOI: https://doi.org/10.2210/pdb5G49/pdb

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


• Deposited: 2016-05-06 Released: 2016-12-07 
• Deposition Author(s): Gnesutta, N., Saad, D., Chaves-Sanjuan, A., Mantovani, R., Nardini, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.200 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Crystal Structure of the Arabidopsis thaliana L1L/NF-YC3 Histone-fold Dimer Reveals Specificities of the LEC1 Family of NF-Y Subunits in Plants.

Gnesutta, N., Saad, D., Chaves-Sanjuan, A., Mantovani, R., Nardini, M.

(2017) Mol Plant 10: 645-648

• PubMed: 27871811 
• DOI: https://doi.org/10.1016/j.molp.2016.11.006
• Primary Citation of Related Structures:  
  5G49

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Organizational Affiliation: 

Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 22.82 kDa 
• Atom Count: 1,715 
• Modelled Residue Count: 191 
• Deposited Residue Count: 192 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6	A	97	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q84W66 (Arabidopsis thaliana) Explore Q84W66  Go to UniProtKB:  Q84W66

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3	B	95	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q9ZVL3 (Arabidopsis thaliana) Explore Q9ZVL3  Go to UniProtKB:  Q9ZVL3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth B], E [auth B], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.200 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.344	α = 90
b = 81.691	β = 90
c = 95.998	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Gnesutta, N., Saad, D., Chaves-Sanjuan, A., Mantovani, R., Nardini, M.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-03-15
  Changes: Database references
• Version 1.2: 2017-04-12
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description