8VDH

Human PU.1 ETS-Domain (165-270) Bound to d(AATAGAAGGAAGTGGG) in Ternary Complex with DB2447

• PDB DOI: https://doi.org/10.2210/pdb8VDH/pdb
• NAKB: 8VDH

• Classification: TRANSCRIPTION/DNA
• Organism(s): DNA molecule, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-15 Released: 2024-09-18 
• Deposition Author(s): Terrell, J.R., Ogbonna, E.N., Poon, G.M.K., Wilson, W.D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), 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: 1.64 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structural Characterization of GC Base Pair Recognition by a Diamidine Small Molecule

Ogbonna, E.N., Terrell, J.R., Paul, A., 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: 22.61 kDa 
• Atom Count: 1,643 
• Modelled 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*GP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')	A [auth C]	16	DNA molecule

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AAQ (Subject of Investigation/LOI)	D [auth C]	4,4'-[pyridine-2,6-diylbis(methyleneoxy)]di(benzene-1-carboximidamide) C21 H21 N5 O2 UDMQJIVHWQYKTJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.208 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.049	α = 90
b = 61.062	β = 116.306
c = 44.178	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: 2024-09-18 
Deposition Author(s): Terrell, J.R., Ogbonna, E.N., Poon, G.M.K., Wilson, W.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM111749
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

Revision History  

• Version 1.0: 2024-09-18
  Type: Initial release