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Structure of the full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA

by single particle reconstruction, at 12 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.2, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.2, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1985
TitleStructure of the full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA
MapVDR-RXR DR3 DNA complex
Samplefull human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
KeywordsNuclear receptor, retinoic acid, vitamin D, DNA response element
AuthorsOrlov I, Rochel N, Moras D, Klaholz BP
DateDeposition: 2011-11-08, Header release: 2012-08-01, Map release: 2012-08-01, Last update: 2012-08-01
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.2, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.2, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 31, Issue 2, Page 291-300, Year 2012
TitleStructure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA.
AuthorsIgor Orlov, Natacha Rochel, Dino Moras, Bruno P Klaholz
Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.
KeywordsAmino Acid Sequence, Calcitriol (chemistry), Cryoelectron Microscopy, DNA (chemistry, 9007-49-2), Dimerization, Humans, Ligands, Macromolecular Substances, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Protein Conformation, Protein Interaction Mapping, Protein Structure, Tertiary, Receptors, Calcitriol (chemistry), Recombinant Fusion Proteins (chemistry), Retinoid X Receptor alpha (chemistry), Tretinoin (chemistry), Vitamin D Response Element, alitretinoin (5300-03-8)
LinksDOI: 10.1038/emboj.2011.445, PubMed: 22179700, PMC: PMC3261568
Map
Fileemd_1985.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2 A/pix
= 256. A
128 pix
2 A/pix
= 256. A
128 pix
2 A/pix
= 256. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.5 (by author), 0.2 (movie #1):
Minimum - Maximum: -2.59364676 - 16.3394928
Average (Standard dev.): 0.01883154 (0.34013131)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-63-64-64
Limit646363
Spacing128128128
Unit CellA= B= C: 256 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z222
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-63-64
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.59416.3390.019
Annotation DetailsVDR-RXR DR3 DNA complex
Supplement
Images
Images
Sample
Namefull human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
Number of Components3
Theoretical Mass0.1MDa
Experimental Mass0.1MDa
Component #1: protein - VDR-RXR
Scientific nameVDR-RXR
Oligomeric Detailshetero dimer
Number of Copies1
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Engineered SourceVector: pACYC
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Stainingno staining, cryo on holey carbon film
Specimen Conc0.15 mg/ml
Specimen Support Details300 mesh Cu/Rh
Specimen Stateparticle
BufferDetails: Tris 20 mM pH7.5, NaCl 50 mM, KCl 50 mM, MgCl2 4mM, DTT 5mM
pH: 7.5
Vitrification
Method2 seconds
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 4000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerPRIMESCAN
Number of Digital Images20
Sampling Size5.8
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmcross-common lines
SoftwareIMAGIC
CTF Correctioneach particle
Detailsresolution 12.3A or 9.1 according to FSC at 0.5 or 0.143 cut-off
Resolution By Author12 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections19938
DetailsEMAN-1 boxer semi-automatic selection and visual control of each boxed particle
Atomic Model Fitting
Model #0
Refinement SpaceREAL
SoftwareIMAGIC, pyMOL
DetailsProtocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Refinement Protocolrigid body
PDB Entry ID1DKF
PDB Chain ID1DKF_A
Model #1
Refinement SpaceREAL
DetailsProtocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
SoftwareIMAGIC, pyMOL
Refinement Protocolrigid body
PDB Entry ID1DB1
PDB Chain ID1DB1_A
Model #2
Refinement Protocolrigid body
DetailsProtocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Refinement SpaceREAL
SoftwareIMAGIC, pyMOL
PDB Entry ID1YNW
PDB Chain ID1YNW_A
Model #3
Refinement Protocolrigid body
DetailsProtocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Refinement SpaceREAL
SoftwareIMAGIC, pyMOL
PDB Entry ID2NLL
PDB Chain ID2NLL_A
Download
Data from EMDB
Header (meta data in XML format)emd-1985.xml (8.9 KB)
Map dataemd_1985.map.gz (553.8 KB)
ImagesEMD-1985.png (42.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1985
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.3 KB