3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1985

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, Image by UCSF CHIMERA

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
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
#1
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
Applied SymmetryC1 (asymmetric)
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