6V41

crystal structure of CDY1 chromodomain bound to H3K9me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for the Binding Selectivity of Human CDY Chromodomains.

Dong, C.Liu, Y.Lyu, T.J.Beldar, S.Lamb, K.N.Tempel, W.Li, Y.Li, Z.James, L.I.Qin, S.Wang, Y.Min, J.

(2020) Cell Chem Biol 27: 827

  • DOI: https://doi.org/10.1016/j.chembiol.2020.05.007
  • Primary Citation of Related Structures:  
    2MJ8, 6V2D, 6V2H, 6V2R, 6V2S, 6V3N, 6V41, 6V8W

  • PubMed Abstract: 

    The CDY (chromodomain on the Y) proteins play an essential role in normal spermatogenesis and brain development. Dysregulation of their expression has been linked to male infertility and various neurological diseases. Like the chromodomains of HP1 and Polycomb, the CDY chromodomains also recognize the lysine-methylated ARKS motif embedded in histone and non-histone proteins. Interestingly, the CDY chromodomains exhibit different binding preferences for the lysine-methylated ARKS motif in different sequence contexts. Here, we present the structural basis for selective binding of CDY1 to H3K9me3 and preferential binding of CDYL2 to H3tK27me3 over H3K27me3. In addition, we use a CDYL1/2-selective compound, UNC4850, to gain further insight into the molecular mechanisms underlying CDYL2 binding specificity. Our work also provides critical implications that CDYL1b's role in the regulation of neural development is dependent on its recognition of the lysine-methylated ARKS motif.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Testis-specific chromodomain protein Y 1A [auth AAA]63Homo sapiensMutation(s): 0 
Gene Names: CDY1CDY1ACDY1B
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F8 (Homo sapiens)
Explore Q9Y6F8 
Go to UniProtKB:  Q9Y6F8
PHAROS:  Q9Y6F8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6F8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1 PeptideB [auth QQQ]15Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth AAA]
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
L [auth AAA],
M [auth AAA],
N [auth AAA],
O [auth AAA],
P [auth AAA],
Q [auth AAA],
R [auth AAA],
S [auth AAA],
T [auth AAA],
U [auth QQQ],
V [auth QQQ]
UNKNOWN ATOM OR ION
X
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
B [auth QQQ]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.447α = 90
b = 42.447β = 90
c = 37.195γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-04-15
    Changes: Database references, Structure summary
  • Version 1.2: 2020-06-17
    Changes: Database references
  • Version 1.3: 2020-07-29
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description