5T1I

CBX3 chromo shadow domain in complex with histone H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1.

Liu, Y.Qin, S.Lei, M.Tempel, W.Zhang, Y.Loppnau, P.Li, Y.Min, J.

(2017) J. Biol. Chem. 292: 5655-5664

  • DOI: 10.1074/jbc.M116.768374

  • PubMed Abstract: 
  • Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD in ...

    Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the P X V X L motif but also with a region of histone H3 that bears the similar P XX V X L motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the P XX V X L motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSD γ ) in complex with an H3 peptide suggests that recognition of H3 by CSD γ to some extent resembles CSD-P X V X L interaction. Nevertheless, the prolyl residue of the P XX V X L motif appears to play a role distinct from that of Pro in the known HP1β CSD-P X V X L complexes. We consequently generalize the historical CSD-P X V X L interaction model and expand the search scope for additional CSD binding partners.


    Organizational Affiliation

    From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and.,the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada and jr.min@utoronto.ca.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromobox protein homolog 3
A, B
68Homo sapiensMutation(s): 0 
Gene Names: CBX3
Find proteins for Q13185 (Homo sapiens)
Go to Gene View: CBX3
Go to UniProtKB:  Q13185
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.1
C
15Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, C
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
N7P
Query on N7P
C
L-peptide linkingC7 H11 N O3PRO
AAR
Query on AAR
C
L-PEPTIDE LINKINGC6 H16 N5 OARG
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 40.737α = 90.00
b = 34.971β = 93.32
c = 45.833γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Structure summary
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2017-03-08
    Type: Database references
  • Version 1.4: 2017-04-19
    Type: Database references