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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: 1985
TitleStructure of the full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA
KeywordsNuclear receptor / retinoic acid / vitamin D / DNA response element
Samplefull human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
SourceHomo sapiens / human
Map dataVDR-RXR DR3 DNA complex
Methodsingle particle reconstruction, at 12 Å resolution
AuthorsOrlov I / Rochel N / Moras D / Klaholz BP
CitationEMBO J., 2012, 31, 291-300

EMBO J., 2012, 31, 291-300 StrPapers
Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA.
Igor Orlov / Natacha Rochel / Dino Moras / Bruno P Klaholz

DateDeposition: Nov 8, 2011 / Header (metadata) release: Aug 1, 2012 / Map release: Aug 1, 2012 / Last update: Aug 1, 2012

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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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Supplemental images

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Map

Fileemd_1985.map.gz (map file in CCP4 format, 8193 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2 Å/pix.
= 256. Å
128 pix
2 Å/pix.
= 256. Å
128 pix
2 Å/pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:0.5 (by author), 0.2 (movie #1):
Minimum - Maximum-2.59364676 - 16.3394928
Average (Standard dev.)0.01883154 (0.34013131)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-63-64-64
Limit646363
Spacing128128128
CellA=B=C: 256 Å
α=β=γ: 90 deg.

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
Number of components: 3
MassTheoretical: 100 kDa / Experimental: 100 kDa

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Component #1: protein, VDR-RXR

ProteinName: VDR-RXR / a.k.a: VDR-RXR / Oligomeric Details: hetero dimer / Recombinant expression: Yes / Number of Copies: 1
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pACYC

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.15 mg/ml
Buffer solution: Tris 20 mM pH7.5, NaCl 50 mM, KCl 50 mM, MgCl2 4mM, DTT 5mM
pH: 7.5
Support film300 mesh Cu/Rh
Stainingno staining, cryo on holey carbon film
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 2 seconds / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 20 / Scanner: PRIMESCAN / Sampling size: 5.8 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19938
Details: EMAN-1 boxer semi-automatic selection and visual control of each boxed particle
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: cross-common lines / Software: IMAGIC / CTF correction: each particle
Details: resolution 12.3A or 9.1 according to FSC at 0.5 or 0.143 cut-off
Resolution: 12 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Input PDB model: 1DKF
Chain ID: 1DKF_A
Modeling #2Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Input PDB model: 1DB1
Chain ID: 1DB1_A
Modeling #3Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Input PDB model: 1YNW
Chain ID: 1YNW_A
Modeling #4Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
Input PDB model: 2NLL
Chain ID: 2NLL_A

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