6V2H

Crystal structure of CDYL2 in complex with H3tK27me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 827-838.e7

  • DOI: 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 ...

    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

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei 430079, China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: jr.min@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chromodomain Y-like protein 2
A, C, E, G, I, K
A, C, E, G, I, K
62Homo sapiensMutation(s): 0 
Gene Names: CDYL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8U2 (Homo sapiens)
Explore Q8N8U2 
Go to UniProtKB:  Q8N8U2
PHAROS:  Q8N8U2
GTEx:  ENSG00000166446 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N8U2
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3tK27me3
B, D, F, H, J, L
B, D, F, H, J, L
14Homo sapiensMutation(s): 0 
Gene Names: 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
IA [auth G],
M [auth A],
OA [auth I],
T [auth C],
TA [auth K],
IA [auth G],
M [auth A],
OA [auth I],
T [auth C],
TA [auth K],
V [auth E]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
GA [auth E],
HA [auth E],
JA [auth G],
KA [auth G],
LA [auth G],
MA [auth G],
N [auth A],
NA [auth H],
O [auth A],
P [auth A],
PA [auth I],
Q [auth A],
QA [auth I],
R [auth B],
RA [auth J],
S [auth B],
SA [auth J],
U [auth C],
UA [auth K],
W [auth E],
X [auth E],
Y [auth E],
Z [auth E]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B, D, F, H, J, L
B, D, F, H, J, L
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: H 3
  • Diffraction Data DOI: 10.18430/m36v2h Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.75α = 90
b = 210.75β = 90
c = 67.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data reduction
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: 2020-06-17
    Changes: Database references, Refinement description
  • Version 1.2: 2020-07-29
    Changes: Database references, Derived calculations