2Q3Y | pdb_00002q3y

Ancestral Corticiod Receptor in Complex with DOC

• PDB DOI: https://doi.org/10.2210/pdb2Q3Y/pdb

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


• Deposited: 2007-05-30 Released: 2007-09-04 
• Deposition Author(s): Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., Thornton, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an ancient protein: evolution by conformational epistasis

Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., Thornton, J.W.

(2007) Science 317: 1544-1548

• PubMed: 17702911 
• DOI: https://doi.org/10.1126/science.1142819
• Primary Citation Related Structures: 
  2Q1H, 2Q1V, 2Q3Y


• PubMed Abstract: 
  

  The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.

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Organizational Affiliation: 
• Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.41 kDa 
• Atom Count: 2,196 
• Modeled Residue Count: 254 
• Deposited Residue Count: 259 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancestral Corticiod Receptor	A	249	unidentified	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor 0B2	B	10	Homo sapiens	Mutation(s): 0  Gene Names: NR0B2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15466 (Homo sapiens) Explore Q15466  Go to UniProtKB:  Q15466
PHAROS:  Q15466 GTEx:  ENSG00000131910

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1CA	C [auth A]	DESOXYCORTICOSTERONE C21 H30 O3 ZESRJSPZRDMNHY-YFWFAHHUSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.995	α = 90
b = 78.995	β = 90
c = 112.467	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Ortlund, E.A., Bridgham, J.T., Redinbo, M.R., Thornton, J.W.

Revision History  

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description