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- EMDB-1985: Structure of the full human RXR-VDR nuclear receptor heterodimer ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1985
TitleStructure of the full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA
Map dataVDR-RXR DR3 DNA complex
Sample
  • Sample: full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
  • Protein or peptide: VDR-RXR
KeywordsNuclear receptor / retinoic acid / vitamin D / DNA response element
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 12.0 Å
AuthorsOrlov I / Rochel N / Moras D / Klaholz BP
CitationJournal: EMBO J / Year: 2012
Title: Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA.
Authors: Igor Orlov / Natacha Rochel / Dino Moras / Bruno P Klaholz /
Abstract: Transcription regulation by steroid hormones and other metabolites is mediated by nuclear receptors (NRs) such as the vitamin D and retinoid X receptors (VDR and RXR). Here, we present the cryo ...Transcription regulation by steroid hormones and other metabolites is mediated by nuclear receptors (NRs) such as the vitamin D and retinoid X receptors (VDR and RXR). Here, we present the cryo electron microscopy (cryo-EM) structure of the heterodimeric complex of the liganded human RXR and VDR bound to a consensus DNA response element forming a direct repeat (DR3). The cryo-EM map of the 100-kDa complex allows positioning the individual crystal structures of ligand- and DNA-binding domains (LBDs and DBDs). The LBDs are arranged perpendicular to the DNA and are located asymmetrically at the DNA 5'-end of the response element. The structure reveals that the VDR N-terminal A/B domain is located close to the DNA. The hinges of both VDR and RXR are fully visible and hold the complex in an open conformation in which co-regulators can bind. The asymmetric topology of the complex provides the structural basis for RXR being an adaptive partner within NR heterodimers, while the specific helical structure of VDR's hinge connects the 3'-bound DBD with the 5'-bound LBD and thereby serves as a conserved linker of defined length sensitive to mutational deletion.
History
DepositionNov 8, 2011-
Header (metadata) releaseAug 1, 2012-
Map releaseAug 1, 2012-
UpdateAug 1, 2012-
Current statusAug 1, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1985.png

Downloads & links

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Map

FileDownload / File: emd_1985.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVDR-RXR DR3 DNA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 128 pix.
= 256. Å		2 Å/pix.
x 128 pix.
= 256. Å		2 Å/pix.
x 128 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.2
Minimum - Maximum-2.59364676 - 16.339492799999999
Average (Standard dev.)0.01883154 (±0.34013131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-63-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-63-64
NC/NR/NS128128128
D min/max/mean-2.59416.3390.019

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Supplemental data

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Sample components

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Entire : full human RXR-VDR nuclear receptor heterodimer complex with its ...

EntireName: full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
Components
  • Sample: full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
  • Protein or peptide: VDR-RXR

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Supramolecule #1000: full human RXR-VDR nuclear receptor heterodimer complex with its ...

SupramoleculeName: full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa

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Macromolecule #1: VDR-RXR

MacromoleculeName: VDR-RXR / type: protein_or_peptide / ID: 1 / Name.synonym: VDR-RXR / Number of copies: 1 / Oligomeric state: hetero dimer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pACYC

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Details: Tris 20 mM pH7.5, NaCl 50 mM, KCl 50 mM, MgCl2 4mM, DTT 5mM
StainingType: NEGATIVE / Details: no staining, cryo on holey carbon film
GridDetails: 300 mesh Cu/Rh
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 2 seconds

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5.8 µm / Number real images: 20 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsEMAN-1 boxer semi-automatic selection and visual control of each boxed particle
CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC
Details: resolution 12.3A or 9.1 according to FSC at 0.5 or 0.143 cut-off
Number images used: 19938

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Atomic model buiding 1

Initial modelPDB ID:

1dkf


Chain - Chain ID: A
SoftwareName: IMAGIC, pyMOL
DetailsPDBEntryID_givenInChain. Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

1db1


Chain - Chain ID: A
SoftwareName: IMAGIC, pyMOL
DetailsPDBEntryID_givenInChain. Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 3

Initial modelPDB ID:

1ynw


Chain - Chain ID: A
SoftwareName: IMAGIC, pyMOL
DetailsPDBEntryID_givenInChain. Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 4

Initial modelPDB ID:

2nll


Chain - Chain ID: A
SoftwareName: IMAGIC, pyMOL
DetailsPDBEntryID_givenInChain. Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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