9CMB | pdb_00009cmb

Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG)

• PDB DOI: https://doi.org/10.2210/pdb9CMB/pdb
• NAKB: 9CMB

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


• Deposited: 2024-07-13 Released: 2025-06-18 
• 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), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Human PU.1 ETS Domain (165-270) bound to d(AATAAAAGGAAGTGGG)

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)

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.53 kDa 
• Atom Count: 2,909 
• Modeled Residue Count: 246 
• Deposited Residue Count: 276 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor PU.1	A, C	106	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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')	B, D	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')	E, F	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.954	α = 90
b = 102.731	β = 111.651
c = 55.753	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: 2025-06-18 
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137160

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release