3WTQ | pdb_00003wtq

Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

• PDB DOI: https://doi.org/10.2210/pdb3WTQ/pdb

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


• Deposited: 2014-04-15 Released: 2015-04-15 
• Deposition Author(s): Nakabayashi, M., Inaba, Y., Itoh, T., Anami, Y., Ikura, T., Ito, N., Yamamoto, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.275 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

Nakabayashi, M., Inaba, Y., Itoh, T., Anami, Y., Ikura, T., Ito, N., Yamamoto, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.64 kDa 
• Atom Count: 2,159 
• Modeled Residue Count: 251 
• Deposited Residue Count: 284 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	271	Rattus norvegicus	Mutation(s): 0  Gene Names: Vdr, Nr1i1
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053  Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mediator of RNA polymerase II transcription subunit 1	B [auth C]	13	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YS9	C [auth A]	(1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol C31 H52 O3 RSXHMKSDJHHTDU-VWOHJUMJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.275 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.286	α = 90
b = 43.851	β = 96.18
c = 42.321	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Nakabayashi, M., Inaba, Y., Itoh, T., Anami, Y., Ikura, T., Ito, N., Yamamoto, K.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations