9YNZ | pdb_00009ynz

Human PU.1 ETS-Domain (165-270) Bound to d(5'-AATAAGCGGAAGTGGG-3') d(5'-TCCCACT*CPD*CGCTTAT-3')

• PDB DOI: https://doi.org/10.2210/pdb9YNZ/pdb
• NAKB: 9YNZ

• Classification: TRANSCRIPTION
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-13 Released: 2025-10-22 
• Deposition Author(s): Terrell, J.R., Poon, G.M.K.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), 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: 2.05 Å
• R-Value Free: 
  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

UV lesion binding and repair inhibition by ETS-family transcription factors

Sivapragasam, S., Terrell, J.R., Germann, M.W., Morledge-Hampton, B., Adhikari, S.P., Brown, M., Hrdlicka, P.J., Wyrick, J.J., 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: 22.25 kDa 
• Atom Count: 1,445 
• Modeled Residue Count: 121 
• Deposited Residue Count: 137 
• 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]	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: 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(P*CP*CP*CP*AP*CP*T*(CPD)P*CP*GP*CP*TP*TP*AP*T)-3')	B [auth D]	15	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.244 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.966	α = 90
b = 58.879	β = 117.593
c = 45.925	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: 2025-10-22 
Deposition Author(s): Terrell, J.R., Poon, G.M.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES035139
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL155178
National Science Foundation (NSF, United States)	United States	2028902

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release