5BSA

Structure of histone H3/H4 in complex with Spt2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.61 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 

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:  
    5BSA, 5BS7

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2AB110Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4CD102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Explore P62799 
Go to UniProtKB:  P62799
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein SPT2 homologEF115Homo sapiensMutation(s): 0 
Gene Names: SPTY2D1
Find proteins for Q68D10 (Homo sapiens)
Explore Q68D10 
Go to UniProtKB:  Q68D10
NIH Common Fund Data Resources
PHAROS  Q68D10
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
E,FL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.61 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.243 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.351α = 90
b = 128.351β = 90
c = 116.814γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
SHELXDEphasing
PHASERphasing
MOLREPphasing
HKL-2000data reduction

Structure Validation

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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
    Changes: Database references, Derived calculations, Refinement description, Source and taxonomy