+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6259 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | ERE-DNA/ERalpha/SRC-3/p300 complex with antibody | |||||||||
Map data | ER complex with antibody | |||||||||
Sample |
| |||||||||
Keywords | Estrogen Receptor | |||||||||
Function / homology | transcription regulator complex Function and homology information | |||||||||
Biological species | Homo sapiens (human) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 47.0 Å | |||||||||
Authors | Yi P / Wang Z / Feng Q / Pintilie GD / Foulds CE / Lanz RB / Ludtke SJ / Schmid MF / Chiu W / O'Malley BW | |||||||||
Citation | Journal: Mol Cell / Year: 2015 Title: Structure of a biologically active estrogen receptor-coactivator complex on DNA. Authors: Ping Yi / Zhao Wang / Qin Feng / Grigore D Pintilie / Charles E Foulds / Rainer B Lanz / Steven J Ludtke / Michael F Schmid / Wah Chiu / Bert W O'Malley / Abstract: Estrogen receptor (ER/ESR1) is a transcription factor critical for development, reproduction, metabolism, and cancer. ER function hinges on its ability to recruit primary and secondary coactivators, ...Estrogen receptor (ER/ESR1) is a transcription factor critical for development, reproduction, metabolism, and cancer. ER function hinges on its ability to recruit primary and secondary coactivators, yet structural information on the full-length receptor-coactivator complex to complement preexisting and sometimes controversial biochemical information is lacking. Here, we use cryoelectron microscopy (cryo-EM) to determine the quaternary structure of an active complex of DNA-bound ERα, steroid receptor coactivator 3 (SRC-3/NCOA3), and a secondary coactivator (p300/EP300). Our structural model suggests the following assembly mechanism for the complex: each of the two ligand-bound ERα monomers independently recruits one SRC-3 protein via the transactivation domain of ERα; the two SRC-3s in turn bind to different regions of one p300 protein through multiple contacts. We also present structural evidence for the location of activation function 1 (AF-1) in a full-length nuclear receptor, which supports a role for AF-1 in SRC-3 recruitment. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6259.map.gz | 15.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6259-v30.xml emd-6259.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | 400_6259.gif 80_6259.gif | 33.6 KB 3.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6259 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6259 | HTTPS FTP |
-Validation report
Summary document | emd_6259_validation.pdf.gz | 79.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6259_full_validation.pdf.gz | 78.5 KB | Display | |
Data in XML | emd_6259_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6259 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6259 | HTTPS FTP |
-Related structure data
Related structure data | 6241C 6260C 6261C 6262C 6263C 6264C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_6259.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | ER complex with antibody | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : ERalpha/SRC-3/p300 complex with antibody 1 (to p300)
Entire | Name: ERalpha/SRC-3/p300 complex with antibody 1 (to p300) |
---|---|
Components |
|
-Supramolecule #1000: ERalpha/SRC-3/p300 complex with antibody 1 (to p300)
Supramolecule | Name: ERalpha/SRC-3/p300 complex with antibody 1 (to p300) / type: sample / ID: 1000 / Number unique components: 4 |
---|---|
Molecular weight | Experimental: 950 KDa / Theoretical: 920 KDa |
-Macromolecule #1: estrogen receptor alpha
Macromolecule | Name: estrogen receptor alpha / type: protein_or_peptide / ID: 1 / Name.synonym: ERalpha / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
Sequence | GO: transcription regulator complex |
-Macromolecule #2: steroid receptor coactivator-3
Macromolecule | Name: steroid receptor coactivator-3 / type: protein_or_peptide / ID: 2 / Name.synonym: SRC-3 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
Sequence | GO: transcription regulator complex |
-Macromolecule #3: histone acetyltransferase p300
Macromolecule | Name: histone acetyltransferase p300 / type: protein_or_peptide / ID: 3 / Name.synonym: EP300 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
Sequence | GO: transcription regulator complex |
-Macromolecule #4: p300 antibody
Macromolecule | Name: p300 antibody / type: protein_or_peptide / ID: 4 / Recombinant expression: No / Database: NCBI |
---|---|
Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
---|---|
Buffer | pH: 7.5 Details: 100 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2, 0.025% Triton X-100, 1mM DTT |
Grid | Details: 200 mesh grid with continuous carbon film |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1 second before plunging. |
-Electron microscopy
Microscope | JEOL 2200FS |
---|---|
Temperature | Min: 90 K / Max: 105 K / Average: 95 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification. |
Date | Oct 1, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 177 / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: 60 degree holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | Images were processed using EMAN2 |
---|---|
CTF correction | Details: per frame |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3088 |
Final angle assignment | Details: EMAN2 |