5CE6

N-terminal domain of FACT complex subunit SPT16 from Cicer arietinum (chickpea)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure and dynamics of Spt16N-domain of FACT complex from Cicer arietinum.

Are, V.N.Ghosh, B.Kumar, A.Gadre, R.Makde, R.D.

(2016) Int J Biol Macromol 88: 36-43

  • DOI: 10.1016/j.ijbiomac.2016.03.029
  • Primary Citation of Related Structures:  
    5CE6

  • PubMed Abstract: 
  • The facilitates chromatin transcription (FACT) complex, a heterodimer of SSRP1 and Spt16 proteins, is an essential histone chaperone that transiently reorganizes nucleosomes during transcription, replication and repair. N-terminal domain of Spt16 sub ...

    The facilitates chromatin transcription (FACT) complex, a heterodimer of SSRP1 and Spt16 proteins, is an essential histone chaperone that transiently reorganizes nucleosomes during transcription, replication and repair. N-terminal domain of Spt16 subunit (Spt16N) is strictly conserved in all the known Spt16 orthologs. Genetic studies in yeast have revealed a partially redundant role of Spt16N for the FACT functionality. Here, we report the crystal structure of Spt16N from a plant origin (Spt16Nca, Cicer arietinum) and its comparisons with the known Spt16N structures from yeasts and human. The inter-domain angle in Spt16Nca is significantly different from that of the yeast and human Spt16N structures. Normal mode analysis and classical molecular dynamics simulations reveal inter-domain movement in Spt16Nca and later also shows conformational flexibility of the critical loops. Spt16Nca binds to histone H3/H4 complex, similar to its orthologs from yeast and human origins. Further, conservation of electrostatic surface potentials in Spt16N structures from evolutionary distinct domains of eukaryotes (plant, human and fungi) have provided the potential sites on Spt16N for histone interactions. The structural comparisons with M24 peptidases show that the hydrophobic pocket shielded by a flexible loop of C-terminal domain of Spt16N that may be functionally important.


    Organizational Affiliation

    High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India. Electronic address: ravimakde@rrcat.gov.in.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACT-Spt16A480Cicer arietinumMutation(s): 0 
Gene Names: LOC101489759
Find proteins for A0A182DWB2 (Cicer arietinum)
Explore A0A182DWB2 
Go to UniProtKB:  A0A182DWB2
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.019α = 90
b = 69.112β = 102.92
c = 71.587γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata processing
MAR345dtbdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references, Derived calculations