9D2X | pdb_00009d2x

SpiD ETS-domain (168-273) in complex with the DNA sequence d(AATAAAAGGAAGTGGG)

• PDB DOI: https://doi.org/10.2210/pdb9D2X/pdb
• NAKB: 9D2X

• Classification: TRANSCRIPTION/DNA
• Organism(s): synthetic construct, Rostroraja eglanteria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-09 Released: 2024-10-30 
• Deposition Author(s): Terrell, J.R., Vernon, T.N., 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: 2.29 Å
• R-Value Free: 
  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

The Structure of the DNA-binding Domain of the Class III ETS-Family Member SpiD from Raja eglanteria

Terrell, J.R., Vernon, T.N., Poon, G.M.K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.63 kDa 
• Atom Count: 2,831 
• Modeled Residue Count: 240 
• Deposited Residue Count: 278 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SpiD	C [auth F], F [auth E]	107	Rostroraja eglanteria	Mutation(s): 0
UniProt
Find proteins for Q9DEW5 (Rostroraja eglanteria) Explore Q9DEW5  Go to UniProtKB:  Q9DEW5

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], D [auth A]	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], E [auth B]	16	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	G [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.270 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.934	α = 79.209
b = 42.939	β = 81.529
c = 62.534	γ = 76.185

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: 2024-10-30 
Deposition Author(s): Terrell, J.R., Vernon, T.N., 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	MCB2028902
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM137160

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release