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- EMDB-22079: EM Structure of Full-Length Androgen Receptor and DNA Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22079
TitleEM Structure of Full-Length Androgen Receptor and DNA Complex
Map dataAR/ARE-DNA complex.
Sample
  • Complex: AR/ARE-DNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsYu X / Yi P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD8818 United States
Welch FoundationQ-1967-20180324 United States
CitationJournal: Mol Cell / Year: 2020
Title: Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes.
Authors: Xinzhe Yu / Ping Yi / Ross A Hamilton / Hong Shen / Muyuan Chen / Charles E Foulds / Michael A Mancini / Steven J Ludtke / Zhao Wang / Bert W O'Malley /
Abstract: Steroid receptors activate gene transcription by recruiting coactivators to initiate transcription of their target genes. For most nuclear receptors, the ligand-dependent activation function domain-2 ...Steroid receptors activate gene transcription by recruiting coactivators to initiate transcription of their target genes. For most nuclear receptors, the ligand-dependent activation function domain-2 (AF-2) is a primary contributor to the nuclear receptor (NR) transcriptional activity. In contrast to other steroid receptors, such as ERα, the activation function of androgen receptor (AR) is largely dependent on its ligand-independent AF-1 located in its N-terminal domain (NTD). It remains unclear why AR utilizes a different AF domain from other receptors despite that NRs share similar domain organizations. Here, we present cryoelectron microscopy (cryo-EM) structures of DNA-bound full-length AR and its complex structure with key coactivators, SRC-3 and p300. AR dimerization follows a unique head-to-head and tail-to-tail manner. Unlike ERα, AR directly contacts a single SRC-3 and p300. The AR NTD is the primary site for coactivator recruitment. The structures provide a basis for understanding assembly of the AR:coactivator complex and its domain contributions for coactivator assembly and transcriptional regulation.
History
DepositionMay 29, 2020-
Header (metadata) releaseJul 15, 2020-
Map releaseJul 15, 2020-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22079.png

Downloads & links

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Map

FileDownload / File: emd_22079.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAR/ARE-DNA complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 200 pix.
= 278. Å		1.39 Å/pix.
x 200 pix.
= 278. Å		1.39 Å/pix.
x 200 pix.
= 278. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.011522781 - 0.046787523
Average (Standard dev.)0.0011290691 (±0.0041212)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 278.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z278.000278.000278.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0120.0470.001

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Supplemental data

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Additional map: AR/ARE-DNA complex with one AR-Ab2 antibody binding. AR-Ab2...

Fileemd_22079_additional_1.map
AnnotationAR/ARE-DNA complex with one AR-Ab2 antibody binding. AR-Ab2 recognizes the region adjacent to the FXXLF motif (residues 23-27).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: AR/ARE-DNA complex with two AR-Ab1 antibodies binding. AR-Ab1...

Fileemd_22079_additional_2.map
AnnotationAR/ARE-DNA complex with two AR-Ab1 antibodies binding. AR-Ab1 recognizes AR NTD (residues 98-503). One Ab1 density is much stronger than the other one.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AR/ARE-DNA complex

EntireName: AR/ARE-DNA complex
Components
  • Complex: AR/ARE-DNA complex

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Supramolecule #1: AR/ARE-DNA complex

SupramoleculeName: AR/ARE-DNA complex / type: complex / ID: 1 / Parent: 0 / Details: Androgen Receptor and DNA complex
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
Molecular weightExperimental: 370 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1958 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 223299
CTF correctionSoftware: (Name: EMAN2 (ver. 2.3), RELION (ver. 3.0))
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 30598
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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