9MWY

Crystal structure of the DNA binding domain of FLI1 in complex with a DNA containing four contiguous GGAA sites

• PDB DOI: https://doi.org/10.2210/pdb9MWY/pdb

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-01-17 Released: 2025-03-12 
• Deposition Author(s): Hou, C., Tsodikov, O.V.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free: 
  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structure and cooperative formation of a FLI1 filament on contiguous GGAA DNA sites

Hou, C., Tsodikov, O.V.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 82.25 kDa 
• Atom Count: 4,115 
• Modelled Residue Count: 432 
• Deposited Residue Count: 630 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Friend leukemia integration 1 transcription factor	A, B [auth D], C, D [auth L]	145	Homo sapiens	Mutation(s): 1  Gene Names: FLI1
UniProt & NIH Common Fund Data Resources
Find proteins for Q01543 (Homo sapiens) Explore Q01543  Go to UniProtKB:  Q01543
PHAROS:  Q01543 GTEx:  ENSG00000151702

Entity ID: 2
Molecule	Chains	Length	Organism	Image
25-mer DNA containing four contiguous GGAA sites, bottom strand	E [auth G]	25	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
25-mer DNA containing four contiguous GGAA sites, top strand	F [auth H]	25	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	G [auth A], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.28 Å
• R-Value Free:  0.281 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.201	α = 90
b = 78.201	β = 90
c = 318.618	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Hou, C., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA243529

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release