3R93

Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.057 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9.

Li, J., Li, Z., Ruan, J., Xu, C., Tong, Y., Pan, P.W., Tempel, W., Crombet, L., Min, J., Zang, J.

(2011) Plos One 6: e25104-e25104

  • DOI: 10.1371/journal.pone.0025104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • M-phase phosphoprotein 8 (MPP8) was initially identified to be a component of the RanBPM-containing large protein complex, and has recently been shown to bind to methylated H3K9 both in vivo and in vitro. MPP8 binding to methylated H3K9 is suggested ...

    M-phase phosphoprotein 8 (MPP8) was initially identified to be a component of the RanBPM-containing large protein complex, and has recently been shown to bind to methylated H3K9 both in vivo and in vitro. MPP8 binding to methylated H3K9 is suggested to recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promote tumor cell motility and invasion. MPP8 contains a chromodomain in its N-terminus, which is used to bind the methylated H3K9.

    Organizational Affiliation: 

    Key Laboratory of Structural Biology, Chinese Academy of Sciences, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M-phase phosphoprotein 8
A, B, C, D
62Homo sapiensMutation(s): 0 
Gene Names: MPHOSPH8 (MPP8)
Find proteins for Q99549 (Homo sapiens)
Go to Gene View: MPHOSPH8
Go to UniProtKB:  Q99549
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3K9Me3 peptide
E, F, G, H
15Homo sapiensMutation(s): 0 
Gene Names: HIST2H3A, HIST2H3C, HIST2H3D (H3F2, H3FM)
Find proteins for Q71DI3 (Homo sapiens)
Go to Gene View: HIST2H3A HIST2H3C HIST2H3D
Go to UniProtKB:  Q71DI3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX
Download SDF File 
Download CCD File 
A, C, D
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E, F, G, H
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.057 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.148α = 90.00
b = 74.005β = 90.00
c = 72.609γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-19
    Type: Database references
  • Version 1.3: 2012-03-21
    Type: Database references
  • Version 1.4: 2017-11-08
    Type: Refinement description