7QP4 | pdb_00007qp4

Complex of a Gemini-cholesterol analogue with Retinoid-related Orphan Receptor gamma

• PDB DOI: https://doi.org/10.2210/pdb7QP4/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-02 Released: 2022-12-14 
• Deposition Author(s): Rochel, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Development of novel Gemini-cholesterol analogues for retinoid-related orphan receptors

Gomez-Bouzo, U., Fall, A., Osz, J., Fall, Y., Rochel, N., Santalla, H.

(2022) Org Chem Front 9: 1522-1530

• DOI: https://doi.org/10.1039/D2QO00040G

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 63.08 kDa 
• Atom Count: 4,120 
• Modeled Residue Count: 469 
• Deposited Residue Count: 533 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor ROR-gamma	A, B	259	Homo sapiens	Mutation(s): 0  Gene Names: RORC, NR1F3, RORG, RZRG
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449  Go to UniProtKB:  P51449
PHAROS:  P51449 GTEx:  ENSG00000143365

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIS-VAL-GLU-ARG-LEU-GLN-ILE-PHE-GLN-HIS-LEU-HIS-PRO-ILE-VAL	C [auth P]	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P51449 (Homo sapiens) Explore P51449  Go to UniProtKB:  P51449
PHAROS:  P51449 GTEx:  ENSG00000143365

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ECK (Subject of Investigation/LOI)	F [auth A], I [auth B]	(3~{S},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-17-[(6~{R})-2,10-dimethyl-2-oxidanyl-undecan-6-yl]-10,13-dimethyl-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-ol C32 H56 O2 MDQUOZBEMDXUCO-PTHRTHQKSA-N
ACT	D [auth A], E [auth A], G [auth B], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.237 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.381	α = 90
b = 99.381	β = 90
c = 129.308	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Rochel, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description