9CK2 | pdb_00009ck2

Human PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG)

• PDB DOI: https://doi.org/10.2210/pdb9CK2/pdb
• NAKB: 9CK2

• Classification: DNA BINDING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-08 Released: 2025-05-21 
• Deposition Author(s): Poon, G.M.K.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Human PU.1 minimal ETS Domain (165-258) bound to d(AATAAGCGGAAGTGGG)

Poon, G.M.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 20.89 kDa 
• Atom Count: 1,682 
• Modeled Residue Count: 122 
• Deposited Residue Count: 126 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor PU.1	C [auth F]	94	Homo sapiens	Mutation(s): 0  Gene Names: SPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P17947 (Homo sapiens) Explore P17947  Go to UniProtKB:  P17947
PHAROS:  P17947 GTEx:  ENSG00000066336

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*AP*GP*CP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')	A [auth C]	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*GP*CP*TP*TP*AP*T)-3')	B [auth D]	16	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.871	α = 90
b = 60.569	β = 116.593
c = 44.292	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Poon, G.M.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL155178
National Science Foundation (NSF, United States)	United States	MCB 2028902

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release