Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 9.25 kDa 
• Atom Count: 648 
• Modelled Residue Count: 73 
• Deposited Residue Count: 78 
• Unique protein chains: 2

6V41

crystal structure of CDY1 chromodomain bound to H3K9me3

• PDB DOI: 10.2210/pdb6V41/pdb
• Entry: 6V41 supersedes: 6UHG

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-11-27 Released: 2019-12-25 
• Deposition Author(s): Qin, S., Tempel, W., Walker, J.R., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

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

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

• PubMed: 32470319 
• 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. 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Testis-specific chromodomain protein Y 1	A [auth AAA]	63	Homo sapiens	Mutation(s): 0  Gene Names: CDY1, CDY1A, CDY1B 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 GTEx:  ENSG00000172288 ENSG00000172352

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1 Peptide	B [auth QQQ]	15	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	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
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B [auth QQQ]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.215 
• R-Value Work: 0.192 
• Space Group: P 4₃
• Diffraction Data DOI: 10.18430/m36uhg Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.447	α = 90
b = 42.447	β = 90
c = 37.195	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-11-27 
• Released Date: 2019-12-25 
Deposition Author(s): Qin, S., Tempel, W., Walker, J.R., Arrowsmith, C.H., Bountra, C., Edwards, A.M., Min, J., Structural Genomics Consortium, Structural Genomics Consortium (SGC)
• This entry supersedes: 6UHG

Revision History  

• 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