5BS7

Structure of histone H3/H4 in complex with Spt2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
111Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C, D
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein SPT2 homolog
E, F
115Homo sapiensMutation(s): 0 
Gene Names: SPTY2D1
Find proteins for Q68D10 (Homo sapiens)
Go to Gene View: SPTY2D1
Go to UniProtKB:  Q68D10
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.230 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 121.205α = 90.00
b = 121.205β = 90.00
c = 118.503γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Leukemia & Lymphoma SocietyUnited StatesLLS-SCOR 7132-08
STARR Foundation grantUnited StatesI5-A554
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403
NIH ORIP HEI grantUnited StatesS10 RR029205

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence