6BSE | pdb_00006bse

Glucocorticoid receptor bound to high cooperativity monomer sequence

• PDB DOI: https://doi.org/10.2210/pdb6BSE/pdb
• NAKB: 6BSE

• Classification: GENE REGULATION
• Organism(s): Saguinus oedipus, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-12-02 Released: 2018-12-05 
• Deposition Author(s): Pufall, M.A.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Cancer Institute (NIH/NCI), Carver Charitable Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

General and sequence-specific roles for DNA in glucocorticoid receptor DNA-binding stoichiometry

Pufall, M.A., Zhang, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 30.41 kDa 
• Atom Count: 1,866 
• Modeled Residue Count: 177 
• Deposited Residue Count: 214 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	A, B	91	Saguinus oedipus	Mutation(s): 0  Gene Names: NR3C1, GRL
UniProt
Find proteins for P79269 (Saguinus oedipus) Explore P79269  Go to UniProtKB:  P79269

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*AP*AP*AP*AP*GP*TP*AP*CP*AP*CP*GP*TP*GP*G)-3')	C	16	synthetic construct

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.447	α = 90
b = 95.172	β = 90
c = 104.719	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: 2018-12-05 
Deposition Author(s): Pufall, M.A.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB 1552862
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	K99/R00 CO149088
Carver Charitable Trust	United States	01-224

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description