5BSA

Structure of histone H3/H4 in complex with Spt2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.611 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2.

Chen, S.Rufiange, A.Huang, H.Rajashankar, K.R.Nourani, A.Patel, D.J.

(2015) Genes Dev. 29: 1326-1340

  • DOI: 10.1101/gad.261115.115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA ...

    Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA polymerases and that histones H3 and H4 possess their own chaperones dedicated to the recovery of nucleosomes. Here, we determined the crystal structure of the conserved C terminus of human Suppressors of Ty insertions 2 (hSpt2C) chaperone bound to an H3/H4 tetramer. The structural studies demonstrate that hSpt2C is bound to the periphery of the H3/H4 tetramer, mimicking the trajectory of nucleosomal-bound DNA. These structural studies have been complemented with in vitro binding and in vivo functional studies on mutants that disrupt key intermolecular contacts involving two acidic patches and hydrophobic residues on Spt2C. We show that contacts between both human and yeast Spt2C with the H3/H4 tetramer are required for the suppression of H3/H4 exchange as measured by H3K56ac and new H3 deposition. These interactions are also crucial for the inhibition of spurious transcription from within coding regions. Together, our data indicate that Spt2 interacts with the periphery of the H3/H4 tetramer and promotes its recycling in the wake of RNA polymerase.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A, B
110Xenopus laevis
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C, D
102Xenopus laevis
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein SPT2 homolog
E, F
115Homo sapiensGene Names: SPTY2D1
Find proteins for Q68D10 (Homo sapiens)
Go to Gene View: SPTY2D1
Go to UniProtKB:  Q68D10
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.611 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.239 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.351α = 90.00
b = 128.351β = 90.00
c = 116.814γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
MOLREPphasing
SHELXDEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-01 
  • Released Date: 2015-07-08 
  • Deposition Author(s): Chen, S., Patel, D.J.

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy