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- PDB-1dsz: STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1dsz
TitleSTRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER IN COMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1
Components
  • (RETINOIC ACID RECEPTOR ...) x 2
  • DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
  • DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / RXR / RAR / nuclear receptor / protein-DNA / retinoic acid / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / embryonic camera-type eye development / chondroblast differentiation / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus ...Sertoli cell fate commitment / positive regulation of binding / trachea cartilage development / ventricular cardiac muscle cell differentiation / embryonic camera-type eye development / chondroblast differentiation / glandular epithelial cell development / negative regulation of granulocyte differentiation / protein kinase B binding / cellular response to corticotropin-releasing hormone stimulus / growth plate cartilage development / positive regulation of T-helper 2 cell differentiation / prostate gland development / negative regulation of cartilage development / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / regulation of hematopoietic progenitor cell differentiation / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone receptor signaling pathway / positive regulation of interleukin-13 production / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of interleukin-5 production / nuclear glucocorticoid receptor binding / Carnitine metabolism / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / response to vitamin A / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / apoptotic cell clearance / limb development / regulation of myelination / protein kinase A binding / ureteric bud development / Signaling by Retinoic Acid / DNA binding domain binding / DNA-binding transcription repressor activity / nuclear steroid receptor activity / heterocyclic compound binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / positive regulation of interleukin-4 production / LBD domain binding / face development / alpha-actinin binding / germ cell development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / retinoic acid receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of cell cycle / cellular response to retinoic acid / response to retinoic acid / Recycling of bile acids and salts / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / mRNA regulatory element binding translation repressor activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / liver development / response to cytokine / neural tube closure / transcription coregulator binding / female pregnancy / hippocampus development / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / regulation of synaptic plasticity / Transcriptional activation of mitochondrial biogenesis / multicellular organism growth / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / mRNA 5'-UTR binding / transcription coactivator binding / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding
Similarity search - Function
: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. ...: / : / Retinoic acid receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear/hormone receptor activator site AF-1 / Nuclear/hormone receptor activator site AF-1 / Retinoid X receptor/HNF4 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Retinoic acid receptor alpha / Retinoic acid receptor RXR-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsRastinejad, F. / Wagner, T. / Zhao, Q. / Khorasanizadeh, S.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1.
Authors: Rastinejad, F. / Wagner, T. / Zhao, Q. / Khorasanizadeh, S.
History
DepositionJan 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3')
A: RETINOIC ACID RECEPTOR ALPHA
B: RETINOIC ACID RECEPTOR RXR-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6548
Polymers29,3934
Non-polymers2624
Water6,089338
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.660, 33.900, 101.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules CD

#1: DNA chain DNA (5'-D(*CP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')


Mass: 4643.037 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*G)-3')


Mass: 4535.946 Da / Num. of mol.: 1 / Source method: obtained synthetically

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RETINOIC ACID RECEPTOR ... , 2 types, 2 molecules AB

#3: Protein RETINOIC ACID RECEPTOR ALPHA / RAR-ALPHA


Mass: 10220.006 Da / Num. of mol.: 1 / Fragment: RESIDUES 82-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P10276
#4: Protein RETINOIC ACID RECEPTOR RXR-ALPHA / RXR-ALPHA


Mass: 9993.584 Da / Num. of mol.: 1 / Fragment: RESIDUES 129-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P19793

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Non-polymers , 2 types, 342 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18-23% PEG 3350, 25 mM Tris buffer, 5 mM MgCl2, 0.4 M NH4CL, RXR and RAR proteins each at 0.45 mM, DNA duplex at 0.45 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris buffer11
2NH4Cl11
3MgCl211
4PEG 335011
5PEG 335012
Crystal grow
*PLUS
Temperature: 8 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.90 mMprotein1drop
20.45 mMDNA1drop
325 mMTris-HCl1drop
418-23 %PEG33501reservoir
525 mMTris-HCl1reservoir
65 mM1reservoirMgCl2
70.4 M1reservoirNH4Cl

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: May 11, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 29834 / Num. obs: 29834 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.17 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 % / Mean I/σ(I) obs: 8.8

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: X-PLOR
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1416 5 %random
Rwork0.198 ---
all0.201 29834 --
obs0.201 28332 --
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 609 4 339 2196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg2.1

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