8UFF | pdb_00008uff

Human PU.1 ETS-Domain (165-270) Bound to d(AATAAAAGGAAGTGGG) in Ternary Complex with DB1976

• PDB DOI: https://doi.org/10.2210/pdb8UFF/pdb
• NAKB: 8UFF

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


• Deposited: 2023-10-04 Released: 2024-10-09 
• Deposition Author(s): Terrell, J.R., Poon, G.M.K., Wilson, W.D.
• 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: 1.66 Å
• R-Value Free: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Structural studies on the PU.1 inhibitory mechanism by diamidine minor groove binders

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Poon, G.M.K., Wilson, W.D.

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: 22.68 kDa 
• Atom Count: 1,644 
• Modeled Residue Count: 123 
• Deposited Residue Count: 138 
• 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*AP*AP*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*TP*TP*TP*TP*AP*T)-3')	B [auth D]	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y5U (Subject of Investigation/LOI)	D	(2M,2'M)-2,2'-(selenophene-2,5-diyl)di(1H-benzimidazole-6-carboximidamide) C20 H16 N8 Se NXECULIQZLOKFU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.913	α = 90
b = 60.292	β = 116.358
c = 44.393	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: 2024-10-09 
Deposition Author(s): Terrell, J.R., Poon, G.M.K., Wilson, W.D.

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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	MCB2028902
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137160
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release