6A8M

N-terminal domain of FACT complex subunit SPT16 from Eremothecium gossypii (Ashbya gossypii)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of 'peptidase' domain of Spt16.

Gaur, N.K.Ghosh, B.Goyal, V.D.Kulkarni, K.Makde, R.D.

(2021) J Biomol Struct Dyn : 1-13

  • DOI: https://doi.org/10.1080/07391102.2021.2021990
  • Primary Citation of Related Structures:  
    6A8M

  • PubMed Abstract: 

    Protein function is encoded in its sequence, manifested in its three-dimensional structure, and facilitated by its dynamics. Studies have suggested that protein structures with higher sequence similarity could have more similar patterns of dynamics. However, such studies of protein dynamics within and across protein families typically rely on coarse-grained models, or approximate metrics like crystallographic B-factors. This study uses µs scale molecular dynamics (MD) simulations to explore the conservation of dynamics among homologs of ∼50 kDa N-terminal module of Spt16 (Spt16N). Spt16N from Saccharomyces cerevisiae (Sc-Spt16N) and three of its homologs with 30-40% sequence identities were available in the PDB. To make our data-set more comprehensive, the crystal structure of an additional homolog (62% sequence identity with Sc-Spt16N) was solved at 1.7 Å resolution. Cumulative MD simulations of 6 µs were carried out on these Spt16N structures and on two additional protein structures with varying degrees of similarity to it. The simulations revealed that correlation in patterns of backbone fluctuations vary linearly with sequence identity. This trend could not be inferred using crystallographic B-factors. Further, normal mode analysis suggested a similar pattern of inter-domain (inter-lobe) motions not only among Spt16N homologs, but also in the M24 peptidase structure. On the other hand, MD simulation results highlighted conserved motions that were found unique for Spt16N protein, this along with electrostatics trends shed light on functional aspects of Spt16N.Communicated by Ramaswamy H. Sarma.


  • Organizational Affiliation

    Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FACT complex subunit SPT16461Eremothecium gossypii ATCC 10895Mutation(s): 0 
Gene Names: SPT16AER360C
UniProt
Find proteins for Q756A7 (Eremothecium gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056))
Explore Q756A7 
Go to UniProtKB:  Q756A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ756A7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.885α = 90
b = 119.885β = 90
c = 76.662γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description