General information
PDB ID 1YNW
Title CRYSTAL STRUCTURE OF VITAMIN D RECEPTOR AND 9-CIS RETINOIC ACID RECEPTOR DNA-BINDING DOMAINS BOUND TO A DR3 RESPONSE ELEMENT
PDB header TRANSCRIPTION/DNA
Date 2005-01-25
Experimental method X-RAY DIFFRACTION
Resolution (A) 3
Kind dna
Organism HOMO SAPIENS
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PDB PDBe MMDB Jena OCA
CATH PDBsum HSSP PDBePISA UniProt
ProteopediA BIPA
Composition of PDB entry and biounits
File: Protein chains: DNA chains: RNA chains: No. of models: Action:
PDB entry:
pdb1ynw.pdb AB CD 0
Biounits:
1ynw.pdb1.pdb AB CD 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
zf-C4 Domain P11473_22-91 1.3e-29 1 CL0167 A 22 91 CD  H-Bb H-Mj L-Bb 
zf-C4 Domain P19793_133-202 1.5e-33 1 CL0167 B 234 302 CD  H-Bb H-Mj S-Mj L-Bb 
SCOP domains
Classification: Protein: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Class: Small proteins
  Fold: Glucocorticoid receptor-like (DNA-binding domain)
    Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
      Family: Nuclear receptor
Vitamin D3 receptor, VDR, DNA-binding domain A 18 113 CD  H-Bb H-Mj L-Bb 
Class: Small proteins
  Fold: Glucocorticoid receptor-like (DNA-binding domain)
    Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
      Family: Nuclear receptor
Retinoid X receptor (RXR-alpha) DNA-binding domain B 235 300 CD  H-Bb H-Mj L-Bb 
GO terms
Protein chains: GO type: GO description:
A=16-125 C cytosol
A=16-125 C nuclear chromatin
A=16-125 C nucleoplasm
A=16-125 C nucleus
A=16-125 C receptor complex
A=16-125 C RNA polymerase II transcription regulator complex
A=16-125 F calcitriol binding
A=16-125 F DNA binding
A=16-125 F DNA-binding transcription factor activity, RNA polymerase II-specific
A=16-125 F lithocholic acid binding
A=16-125 F lithocholic acid receptor activity
A=16-125 F nuclear receptor activity
A=16-125 F retinoid X receptor binding
A=16-125 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
A=16-125 F signaling receptor activity
A=16-125 F transcription factor binding
A=16-125 F zinc ion binding
A=16-125 P bile acid signaling pathway
A=16-125 P calcium ion transport
A=16-125 P cell differentiation
A=16-125 P cell morphogenesis
A=16-125 P cellular calcium ion homeostasis
A=16-125 P cholesterol homeostasis
A=16-125 P decidualization
A=16-125 P intestinal absorption
A=16-125 P lactation
A=16-125 P lipid homeostasis
A=16-125 P lipid metabolic process
A=16-125 P mammary gland branching involved in pregnancy
A=16-125 P multicellular organism development
A=16-125 P negative regulation of cell population proliferation
A=16-125 P negative regulation of gene expression
A=16-125 P negative regulation of keratinocyte proliferation
A=16-125 P negative regulation of transcription by RNA polymerase II
A=16-125 P negative regulation of transcription, DNA-templated
A=16-125 P positive regulation of apoptotic process involved in mammary gland involution
A=16-125 P positive regulation of gene expression
A=16-125 P positive regulation of keratinocyte differentiation
A=16-125 P positive regulation of transcription by RNA polymerase II
A=16-125 P positive regulation of vitamin D 24-hydroxylase activity
A=16-125 P regulation of calcidiol 1-monooxygenase activity
A=16-125 P skeletal system development
A=16-125 P transcription initiation from RNA polymerase II promoter
A=16-125 P vitamin D metabolic process
A=16-125 P vitamin D receptor signaling pathway
B=130-228 C mitochondrion
B=130-228 C nuclear chromatin
B=130-228 C nucleoplasm
B=130-228 C nucleus
B=130-228 C protein-containing complex
B=130-228 C receptor complex
B=130-228 C RNA polymerase II transcription regulator complex
B=130-228 F chromatin DNA binding
B=130-228 F DNA binding domain binding
B=130-228 F DNA-binding transcription factor activity
B=130-228 F DNA-binding transcription factor activity, RNA polymerase II-specific
B=130-228 F double-stranded DNA binding
B=130-228 F enzyme binding
B=130-228 F identical protein binding
B=130-228 F LBD domain binding
B=130-228 F nuclear receptor activity
B=130-228 F nuclear receptor binding
B=130-228 F peptide binding
B=130-228 F retinoic acid binding
B=130-228 F retinoic acid-responsive element binding
B=130-228 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
B=130-228 F RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
B=130-228 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
B=130-228 F sequence-specific DNA binding
B=130-228 F sequence-specific double-stranded DNA binding
B=130-228 F steroid hormone receptor activity
B=130-228 F transcription regulatory region sequence-specific DNA binding
B=130-228 F vitamin D receptor binding
B=130-228 F zinc ion binding
B=130-228 P anatomical structure development
B=130-228 P bile acid and bile salt transport
B=130-228 P camera-type eye development
B=130-228 P cardiac muscle cell proliferation
B=130-228 P cell differentiation
B=130-228 P cholesterol metabolic process
B=130-228 P embryo implantation
B=130-228 P in utero embryonic development
B=130-228 P maternal placenta development
B=130-228 P modulation by virus of host process
B=130-228 P negative regulation of transcription by RNA polymerase II
B=130-228 P peroxisome proliferator activated receptor signaling pathway
B=130-228 P positive regulation of transcription by RNA polymerase II
B=130-228 P positive regulation of transcription, DNA-templated
B=130-228 P positive regulation of translational initiation by iron
B=130-228 P regulation of branching involved in prostate gland morphogenesis
B=130-228 P regulation of lipid metabolic process
B=130-228 P regulation of transcription by RNA polymerase II
B=130-228 P response to retinoic acid
B=130-228 P retinoic acid receptor signaling pathway
B=130-228 P secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development
B=130-228 P transcription initiation from RNA polymerase II promoter
B=130-228 P ventricular cardiac muscle cell differentiation
B=130-228 P ventricular cardiac muscle tissue morphogenesis
Sequences
Download file with secondary structure created by Stride  
1ynw.pdb1.pdb:   [ download sequences in FASTA format ]
C (dna): 
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D (dna): 
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A (protein): 
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B (protein): 
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