9C0O

Crystal structure of DmCfp1 PHD finger bound to H3K4me3

• PDB DOI: https://doi.org/10.2210/pdb9C0O/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Drosophila melanogaster, Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-05-27 Released: 2024-07-03 
• Deposition Author(s): Gregoire, S., Couture, J.F.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.194 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Structural insights into an atypical histone binding mechanism by a PHD finger.

Gregoire, S., Gregoire, J., Yang, Y., Capitani, S., Joshi, M., Sarvan, S., Zaker, A., Ning, Z., Figeys, D., Ulrich, K., Brunzelle, J.S., Mer, A., Couture, J.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 9.94 kDa 
• Atom Count: 711 
• Modelled Residue Count: 72 
• Deposited Residue Count: 81 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CXXC-type zinc finger protein 1	A	66	Drosophila melanogaster	Mutation(s): 0  Gene Names: Cfp1, CG17446
UniProt
Find proteins for Q9W352 (Drosophila melanogaster) Explore Q9W352  Go to UniProtKB:  Q9W352

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	B [auth D]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens) Explore Q6NXT2  Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2 GTEx:  ENSG00000188375

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B [auth D]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.194 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.27	α = 90
b = 43.12	β = 90
c = 47.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
xia2	data reduction
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Gregoire, S., Couture, J.F.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-148533

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release