2HCD | pdb_00002hcd

Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide

PDB DOI: https://doi.org/10.2210/pdb2HCD/pdb

Classification: GENE REGULATION
Organism(s): Danio rerio, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-06-16 Released: 2007-05-01
Deposition Author(s): Ciesielski, F., Rochel, N., Moras, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.260 (Depositor), 0.262 (DCC)
R-Value Work:
0.204 (Depositor), 0.214 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Adaptability of the Vitamin D nuclear receptor to the synthetic ligand Gemini: remodelling the LBP with one side chain rotation

Ciesielski, F., Rochel, N., Moras, D.

(2007) J Steroid Biochem Mol Biol 103: 235-242

PubMed: 17218092 Search on PubMed
DOI: https://doi.org/10.1016/j.jsbmb.2006.12.003
Primary Citation Related Structures:
2HC4, 2HCD

PubMed Abstract:
The crystal structure of the ligand binding domain (LBD) of the wild-type Vitamin D receptor (VDR) of zebrafish bound to Gemini, a synthetic agonist ligand with two identical side chains branching at carbon 20 reveals a ligand-dependent structural rearrangement of the ligand binding pocket (LBP). The rotation of a Leu side chain opens the access to a channel that can accommodate the second side chain of the ligand. The 25% increase of the LBP's volume does not alter the essential agonist features of VDR. The possibility to adapt the LBP to novel ligands with different chemistry and/or structure opens new perspectives in the design of more specifically targeted ligands.

Organizational Affiliation

Département de Biologie et de Génomique Structurales, IGBMC, CNRS/INSERM Université Louis Pasteur, Parc d'innovation BP10142, 67404 Illkirch Cedex, France.

Macromolecule Content

Total Structure Weight: 36.34 kDa
Atom Count: 2,069
Modeled Residue Count: 249
Deposited Residue Count: 317
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D receptor	A	302	Danio rerio	Mutation(s): 0
UniProt
Find proteins for Q9PTN2 (Danio rerio) Explore Q9PTN2 Go to UniProtKB: Q9PTN2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PTN2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SRC-1 from Nuclear receptor coactivator 1	B	15	Homo sapiens	Mutation(s): 0 EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788 Go to UniProtKB: Q15788
PHAROS: Q15788 GTEx: ENSG00000084676
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BIV Query on BIV Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) C₃₂ H₅₄ O₄ WTQXZYVWLNPNEX-LKUPKUSPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.260 (Depositor), 0.262 (DCC)
R-Value Work: 0.204 (Depositor), 0.214 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.859	α = 90
b = 65.859	β = 90
c = 265.018	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-05-01

Deposition Author(s):

Ciesielski, F.

Rochel, N.

Moras, D.

Revision History (Full details and data files)

Version 1.0: 2007-05-01
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-03-03
Changes: Advisory, Database references, Derived calculations, Source and taxonomy
Version 1.4: 2023-10-25
Changes: Advisory, Data collection, Database references, Refinement description