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- EMDB-22080: EM Structure of Full-Length Androgen Receptor Coactivator Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22080
TitleEM Structure of Full-Length Androgen Receptor Coactivator Complex
Map dataAR/ARE-DNA/p300/SRC-3 complex
Sample
  • Complex: AR/ARE-DNA/p300/SRC-3 complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22080.png

Downloads & links

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Map

FileDownload / File: emd_22080.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAR/ARE-DNA/p300/SRC-3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 220 pix.
= 382.8 Å		1.74 Å/pix.
x 220 pix.
= 382.8 Å		1.74 Å/pix.
x 220 pix.
= 382.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.009446999 - 0.05526348
Average (Standard dev.)0.0008093379 (±0.0032232108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 382.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z382.800382.800382.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0090.0550.001

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Supplemental data

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Additional map: AR/ARE-DNA/p300/SRC-3 binding with SRC3-Ab

Fileemd_22080_additional_1.map
AnnotationAR/ARE-DNA/p300/SRC-3 binding with SRC3-Ab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: AR/ARE-DNA/p300/SRC-3 binding with AR-Ab1

Fileemd_22080_additional_2.map
AnnotationAR/ARE-DNA/p300/SRC-3 binding with AR-Ab1
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/p300/SRC-3 complex

EntireName: AR/ARE-DNA/p300/SRC-3 complex
Components
  • Complex: AR/ARE-DNA/p300/SRC-3 complex

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Supramolecule #1: AR/ARE-DNA/p300/SRC-3 complex

SupramoleculeName: AR/ARE-DNA/p300/SRC-3 complex / type: complex / ID: 1 / Parent: 0 / Details: Androgen Receptor coactivator complex
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
Molecular weightExperimental: 800 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
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL 3200FSC
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 5741 / 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

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Image processing

Particle selectionNumber selected: 869561
CTF correctionSoftware: (Name: EMAN2 (ver. 2.3), RELION (ver. 3.0))
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 53198
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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