General information
PDB ID 3DZU
Title INTACT PPAR GAMMA - RXR ALPHA NUCLEAR RECEPTOR COMPLEX ON DNA BOUND WITH BVT.13, 9-CIS RETINOIC ACID AND NCOA2 PEPTIDE
PDB header TRANSCRIPTION/DNA
Date 2008-07-30
Experimental method X-RAY DIFFRACTION
Resolution (A) 3.2
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:
pdb3dzu.pdb ADGE CF 0
Biounits:
3dzu.pdb1.pdb ADGE CF 1
Pfam domains
Name: Type: Domain: E-value: Significance: Clan: Prot. chain: Start res.: End res.: Nuc. chains: Int. mode: Action:
Hormone_recep Domain P19793_263-442 1.9e-37 1 No_clan A 241 442   
zf-C4 Domain P19793_133-202 3.4e-32 1 CL0167 A 133 202 CF  H-Bb H-Mj S-Bb L-Bb 
zf-C4 Domain P37231_137-205 2e-27 1 CL0167 D 109 177 CF  H-Bb H-Mj S-Bb L-Bb 
Hormone_recep Domain P37231_304-486 2.7e-15 1 No_clan D 289 458   
SCOP domains
No SCOP domains
GO terms
Protein chains: GO type: GO description:
A=11-462 C mitochondrion
A=11-462 C nuclear chromatin
A=11-462 C nucleoplasm
A=11-462 C nucleus
A=11-462 C protein-containing complex
A=11-462 C receptor complex
A=11-462 C RNA polymerase II transcription regulator complex
A=11-462 F chromatin DNA binding
A=11-462 F DNA binding domain binding
A=11-462 F DNA-binding transcription factor activity
A=11-462 F DNA-binding transcription factor activity, RNA polymerase II-specific
A=11-462 F double-stranded DNA binding
A=11-462 F enzyme binding
A=11-462 F identical protein binding
A=11-462 F LBD domain binding
A=11-462 F nuclear receptor activity
A=11-462 F nuclear receptor binding
A=11-462 F peptide binding
A=11-462 F retinoic acid binding
A=11-462 F retinoic acid-responsive element binding
A=11-462 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
A=11-462 F RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
A=11-462 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
A=11-462 F sequence-specific DNA binding
A=11-462 F sequence-specific double-stranded DNA binding
A=11-462 F steroid hormone receptor activity
A=11-462 F transcription regulatory region sequence-specific DNA binding
A=11-462 F vitamin D receptor binding
A=11-462 F zinc ion binding
A=11-462 P anatomical structure development
A=11-462 P bile acid and bile salt transport
A=11-462 P camera-type eye development
A=11-462 P cardiac muscle cell proliferation
A=11-462 P cell differentiation
A=11-462 P cholesterol metabolic process
A=11-462 P embryo implantation
A=11-462 P in utero embryonic development
A=11-462 P maternal placenta development
A=11-462 P modulation by virus of host process
A=11-462 P negative regulation of transcription by RNA polymerase II
A=11-462 P peroxisome proliferator activated receptor signaling pathway
A=11-462 P positive regulation of transcription by RNA polymerase II
A=11-462 P positive regulation of transcription, DNA-templated
A=11-462 P positive regulation of translational initiation by iron
A=11-462 P regulation of branching involved in prostate gland morphogenesis
A=11-462 P regulation of lipid metabolic process
A=11-462 P regulation of transcription by RNA polymerase II
A=11-462 P response to retinoic acid
A=11-462 P retinoic acid receptor signaling pathway
A=11-462 P secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development
A=11-462 P transcription initiation from RNA polymerase II promoter
A=11-462 P ventricular cardiac muscle cell differentiation
A=11-462 P ventricular cardiac muscle tissue morphogenesis
D=102-505 C cytosol
D=102-505 C intracellular membrane-bounded organelle
D=102-505 C nuclear chromatin
D=102-505 C nucleoplasm
D=102-505 C nucleus
D=102-505 C perinuclear region of cytoplasm
D=102-505 C protein-containing complex
D=102-505 C RNA polymerase II transcription regulator complex
D=102-505 F activating transcription factor binding
D=102-505 F alpha-actinin binding
D=102-505 F arachidonic acid binding
D=102-505 F chromatin binding
D=102-505 F DNA binding
D=102-505 F DNA binding domain binding
D=102-505 F DNA-binding transcription factor activity
D=102-505 F DNA-binding transcription factor activity, RNA polymerase II-specific
D=102-505 F DNA-binding transcription repressor activity, RNA polymerase II-specific
D=102-505 F double-stranded DNA binding
D=102-505 F drug binding
D=102-505 F E-box binding
D=102-505 F enzyme binding
D=102-505 F estrogen receptor binding
D=102-505 F identical protein binding
D=102-505 F LBD domain binding
D=102-505 F nuclear receptor activity
D=102-505 F nuclear receptor transcription coactivator activity
D=102-505 F peptide binding
D=102-505 F prostaglandin receptor activity
D=102-505 F protein C-terminus binding
D=102-505 F protein phosphatase binding
D=102-505 F protein self-association
D=102-505 F retinoid X receptor binding
D=102-505 F RNA polymerase II repressing transcription factor binding
D=102-505 F RNA polymerase II transcription regulatory region sequence-specific DNA binding
D=102-505 F signaling receptor activity
D=102-505 F transcription factor binding
D=102-505 F transcription regulatory region sequence-specific DNA binding
D=102-505 F zinc ion binding
D=102-505 P activation of cysteine-type endopeptidase activity involved in apoptotic process
D=102-505 P animal organ regeneration
D=102-505 P cell differentiation
D=102-505 P cell fate commitment
D=102-505 P cell maturation
D=102-505 P cellular response to hyperoxia
D=102-505 P cellular response to insulin stimulus
D=102-505 P cellular response to low-density lipoprotein particle stimulus
D=102-505 P cellular response to prostaglandin E stimulus
D=102-505 P cellular response to retinoic acid
D=102-505 P cellular response to vitamin E
D=102-505 P epithelial cell differentiation
D=102-505 P fatty acid metabolic process
D=102-505 P fatty acid oxidation
D=102-505 P glucose homeostasis
D=102-505 P heart development
D=102-505 P hormone-mediated signaling pathway
D=102-505 P innate immune response
D=102-505 P lipid homeostasis
D=102-505 P lipid metabolic process
D=102-505 P lipoprotein transport
D=102-505 P long-chain fatty acid transport
D=102-505 P low-density lipoprotein particle receptor biosynthetic process
D=102-505 P macrophage derived foam cell differentiation
D=102-505 P monocyte differentiation
D=102-505 P negative regulation of acute inflammatory response
D=102-505 P negative regulation of angiogenesis
D=102-505 P negative regulation of blood vessel endothelial cell migration
D=102-505 P negative regulation of cell growth
D=102-505 P negative regulation of cholesterol storage
D=102-505 P negative regulation of collagen biosynthetic process
D=102-505 P negative regulation of gene silencing by miRNA
D=102-505 P negative regulation of inflammatory response
D=102-505 P negative regulation of interferon-gamma-mediated signaling pathway
D=102-505 P negative regulation of macrophage derived foam cell differentiation
D=102-505 P negative regulation of pancreatic stellate cell proliferation
D=102-505 P negative regulation of receptor biosynthetic process
D=102-505 P negative regulation of sequestering of triglyceride
D=102-505 P negative regulation of smooth muscle cell proliferation
D=102-505 P negative regulation of telomerase activity
D=102-505 P negative regulation of transcription by RNA polymerase II
D=102-505 P negative regulation of transcription, DNA-templated
D=102-505 P negative regulation of vascular associated smooth muscle cell proliferation
D=102-505 P negative regulation of vascular endothelial cell proliferation
D=102-505 P peroxisome proliferator activated receptor signaling pathway
D=102-505 P placenta development
D=102-505 P positive regulation of DNA binding
D=102-505 P positive regulation of DNA-binding transcription factor activity
D=102-505 P positive regulation of fat cell differentiation
D=102-505 P positive regulation of fatty acid metabolic process
D=102-505 P positive regulation of fatty acid oxidation
D=102-505 P positive regulation of oligodendrocyte differentiation
D=102-505 P positive regulation of phagocytosis, engulfment
D=102-505 P positive regulation of pri-miRNA transcription by RNA polymerase II
D=102-505 P positive regulation of transcription by RNA polymerase II
D=102-505 P positive regulation of transcription, DNA-templated
D=102-505 P positive regulation of vascular associated smooth muscle cell apoptotic process
D=102-505 P regulation of blood pressure
D=102-505 P regulation of cholesterol transporter activity
D=102-505 P regulation of circadian rhythm
D=102-505 P regulation of lipid metabolic process
D=102-505 P regulation of transcription by RNA polymerase II
D=102-505 P regulation of transcription involved in cell fate commitment
D=102-505 P response to caffeine
D=102-505 P response to cold
D=102-505 P response to drug
D=102-505 P response to estrogen
D=102-505 P response to immobilization stress
D=102-505 P response to lipid
D=102-505 P response to mechanical stimulus
D=102-505 P response to metformin
D=102-505 P response to nutrient
D=102-505 P response to starvation
D=102-505 P response to vitamin A
D=102-505 P retinoic acid receptor signaling pathway
D=102-505 P rhythmic process
D=102-505 P signal transduction
D=102-505 P transcription initiation from RNA polymerase II promoter
D=102-505 P white fat cell differentiation
E/G=685-697 C cytoplasm
E/G=685-697 C nuclear body
E/G=685-697 C nuclear chromatin
E/G=685-697 C nucleoplasm
E/G=685-697 C nucleus
E/G=685-697 C protein-containing complex
E/G=685-697 F aryl hydrocarbon receptor binding
E/G=685-697 F chromatin binding
E/G=685-697 F DNA-binding transcription factor activity, RNA polymerase II-specific
E/G=685-697 F nuclear hormone receptor binding
E/G=685-697 F nuclear receptor binding
E/G=685-697 F nuclear receptor transcription coactivator activity
E/G=685-697 F protein dimerization activity
E/G=685-697 F protein domain specific binding
E/G=685-697 F RNA polymerase II cis-regulatory region sequence-specific DNA binding
E/G=685-697 F RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding
E/G=685-697 F thyroid hormone receptor coactivator activity
E/G=685-697 F transcription coactivator activity
E/G=685-697 P bile acid and bile salt transport
E/G=685-697 P cellular response to hormone stimulus
E/G=685-697 P cellular response to Thyroglobulin triiodothyronine
E/G=685-697 P circadian regulation of gene expression
E/G=685-697 P locomotor rhythm
E/G=685-697 P negative regulation of transcription by RNA polymerase II
E/G=685-697 P positive regulation of transcription by RNA polymerase II
E/G=685-697 P regulation of glucose metabolic process
E/G=685-697 P regulation of lipid metabolic process
E/G=685-697 P regulation of transcription, DNA-templated
E/G=685-697 P response to progesterone
Sequences
Download file with secondary structure created by Stride  
3dzu.pdb1.pdb:   [ download sequences in FASTA format ]
C (dna): 
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F (dna): 
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A (protein): 
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D (protein): 
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E (protein): 
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G (protein): 
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