4ZBJ

UBN1 peptide bound to H3.3/H4/Asf1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.248 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex.

Daniel Ricketts, M.Frederick, B.Hoff, H.Tang, Y.Schultz, D.C.Singh Rai, T.Grazia Vizioli, M.Adams, P.D.Marmorstein, R.

(2015) Nat Commun 6: 7711-7711

  • DOI: 10.1038/ncomms8711

  • PubMed Abstract: 
  • Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to me ...

    Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to mediate H3.3-specific binding and chromatin deposition. Here we demonstrate that the conserved UBN1 Hpc2-related domain (HRD) is a novel H3.3-specific-binding domain. Biochemical and biophysical studies show the UBN1-HRD preferentially binds H3.3/H4 over H3.1/H4. X-ray crystallographic and mutational studies reveal that conserved residues within the UBN1-HRD and H3.3 G90 as key determinants of UBN1-H3.3-binding specificity. Comparison of the structure with the unrelated H3.3-specific chaperone DAXX reveals nearly identical points of contact between the chaperone and histone in the proximity of H3.3 G90, although the mechanism for H3.3 G90 recognition appears to be distinct. This study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA complex.


    Organizational Affiliation

    Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK.,The Wistar Institute, Philadelphia, Pennsylvania, 19104, USA.,1] Institute of Cancer Sciences, CR-UK Beatson Labs, University of Glasgow, Glasgow G61 1BD, UK [2] Institute of Biomedical and Environmental Health Research, University of West of Scotland, Paisley PA1 2BE, UK.,1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.,1] Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [2] Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA [3] Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone chaperone ASF1
A
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ASF1 (CIA1)
Find proteins for P32447 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32447
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
B
77Xenopus laevisMutation(s): 1 
Find proteins for Q6PI79 (Xenopus laevis)
Go to UniProtKB:  Q6PI79
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
C
84Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ubinuclein-1
D
28Homo sapiensMutation(s): 0 
Gene Names: UBN1
Find proteins for Q9NPG3 (Homo sapiens)
Go to Gene View: UBN1
Go to UniProtKB:  Q9NPG3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
D
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.248 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.024α = 90.00
b = 90.024β = 90.00
c = 120.734γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on AgingUnited StatesAG031862
American Heart AssociationUnited States12PRE12030157

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations, Source and taxonomy