9E6E | pdb_00009e6e

Yeast Fzf1 Zn-fingers 1-3 bound to YHB1 26 bp DNA

• PDB DOI: https://doi.org/10.2210/pdb9E6E/pdb
• NAKB: 9E6E

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-29 Released: 2025-11-05 
• Deposition Author(s): Moore, S.A., Ma, C., Xiao, W.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Zn-finger transcription factor Fzf1 binds to its target DNA in a non-canonical manner

Ma, C., Xiao, W., Moore, S.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 101.67 kDa 
• Atom Count: 3,701 
• Modeled Residue Count: 292 
• Deposited Residue Count: 706 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein FZF1	A [auth D], F [auth A]	299	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: FZF1, SUL1, YGL254W, NCR299
UniProt
Find proteins for P32805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32805  Go to UniProtKB:  P32805

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA 1	B [auth E], D [auth B]	27	Saccharomyces cerevisiae

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA 2	C [auth F], E [auth C]	27	Saccharomyces cerevisiae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth D], H [auth D], I [auth D], J [auth A], K [auth A], L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.905	α = 90
b = 66.265	β = 90
c = 174.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Moore, S.A., Ma, C., Xiao, W.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2019-05604
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2011-262138
Canadian Institutes of Health Research (CIHR)	Canada	MOP-126155

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release