+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6263 | |||||||||
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Title | p300 binding with antibody 2 | |||||||||
Map data | p300 bound to antibody 2 | |||||||||
Sample |
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Keywords | P300 / Estrogen Receptor | |||||||||
Function / homology | Function and homology information core promoter sequence-specific DNA binding => GO:0001046 / : / : / : / nuclear receptor binding => GO:0016922 / DNA-binding transcription factor binding => GO:0140297 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / : / positive regulation of sarcomere organization ...core promoter sequence-specific DNA binding => GO:0001046 / : / : / : / nuclear receptor binding => GO:0016922 / DNA-binding transcription factor binding => GO:0140297 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / : / positive regulation of sarcomere organization / protein binding / protein-DNA complex assembly / behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / histone H3K122 acetyltransferase activity / swimming / peptide butyryltransferase activity / positive regulation of glycoprotein biosynthetic process / histone H2B acetyltransferase activity / thigmotaxis / regulation of angiotensin metabolic process / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / protein propionyltransferase activity / response to xenobiotic stimulus => GO:0009410 / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / macrophage derived foam cell differentiation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / STAT family protein binding / histone H4 acetyltransferase activity / cellular response to L-leucine / response to fatty acid / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / response to cobalt ion / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / acetylation-dependent protein binding / NGF-stimulated transcription / STAT3 nuclear events downstream of ALK signaling / histone H3K18 acetyltransferase activity / Polo-like kinase mediated events / digestive tract development / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / regulation of androgen receptor signaling pathway / positive regulation of T-helper 17 cell lineage commitment / regulation of mitochondrion organization / positive regulation by host of viral transcription / face morphogenesis / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / regulation of tubulin deacetylation / nuclear androgen receptor binding / positive regulation of DNA binding / acyltransferase activity / internal protein amino acid acetylation / protein acetylation / fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / PI5P Regulates TP53 Acetylation / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / transcription factor binding / positive regulation of proteolysis / RUNX3 regulates p14-ARF / cellular response to organic cyclic compound / positive regulation of cell size / NF-kappaB binding / histone acetyltransferase complex / positive regulation of collagen biosynthetic process / positive regulation of type I interferon production / Attenuation phase Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 32.0 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6263.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-6263-v30.xml emd-6263.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | 400_6263.gif 80_6263.gif | 30.8 KB 3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6263 | HTTPS FTP |
-Validation report
Summary document | emd_6263_validation.pdf.gz | 79.1 KB | Display | EMDB validaton report |
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Full document | emd_6263_full_validation.pdf.gz | 78.2 KB | Display | |
Data in XML | emd_6263_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6263 | HTTPS FTP |
-Related structure data
Related structure data | 6241C 6259C 6260C 6261C 6262C 6264C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6263.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | p300 bound to antibody 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : p300 bound to antibody 2
Entire | Name: p300 bound to antibody 2 |
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Components |
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-Supramolecule #1000: p300 bound to antibody 2
Supramolecule | Name: p300 bound to antibody 2 / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 400 KDa / Theoretical: 400 KDa |
-Macromolecule #1: histone acetyltransferase p300
Macromolecule | Name: histone acetyltransferase p300 / type: protein_or_peptide / ID: 1 / Name.synonym: EP300 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Molecular weight | Experimental: 300 KDa / Theoretical: 300 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9 |
Sequence | UniProtKB: Histone acetyltransferase p300 GO: chromatin, cytoplasm, histone acetyltransferase complex, nucleoplasm, nucleus, protein-DNA complex, transcription regulator complex, acetyltransferase activity, DNA-binding transcription factor ...GO: chromatin, cytoplasm, histone acetyltransferase complex, nucleoplasm, nucleus, protein-DNA complex, transcription regulator complex, acetyltransferase activity, DNA-binding transcription factor binding => GO:0140297, nuclear androgen receptor binding, antigen binding, beta-catenin binding, chromatin binding, chromatin DNA binding, core promoter sequence-specific DNA binding => GO:0001046, DNA binding, histone acetyltransferase activity, lysine N-acetyltransferase activity, acting on acetyl phosphate as donor, nuclear receptor binding => GO:0016922, protein binding, RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629, RNA polymerase II cis-regulatory region sequence-specific DNA binding, transcription coactivator activity, transcription factor binding, acyltransferase activity, zinc ion binding, apoptotic process, cellular response to hydrogen peroxide, cellular response to hypoxia, cellular response to organic cyclic compound, chromatin organization, circadian rhythm, digestive tract development, G2/M transition of mitotic cell cycle, heart development, GO: 0043969, GO: 0043967, innate immune response, internal peptidyl-lysine acetylation, internal protein amino acid acetylation, intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator, liver development, lung development, mitotic cell cycle, N-terminal peptidyl-lysine acetylation, negative regulation of transcription by RNA polymerase II, nervous system development, Notch signaling pathway, animal organ morphogenesis, positive regulation by host of viral transcription, positive regulation of axon extension, GO: 0010942, positive regulation of cell size, positive regulation of collagen biosynthetic process, positive regulation of DNA binding, positive regulation of glycoprotein biosynthetic process, positive regulation of protein binding, GO: 0033160, positive regulation of protein phosphorylation, positive regulation of protein secretion, positive regulation of proteolysis, positive regulation of sarcomere organization, positive regulation of DNA-binding transcription factor activity, positive regulation of transcription by RNA polymerase II, positive regulation of translation, positive regulation of type I interferon production, phosphatidylinositol 3-kinase/protein kinase B signal transduction, protein-DNA complex assembly, regulation of androgen receptor signaling pathway, regulation of angiotensin metabolic process, regulation of cell cycle, GO: 0061418, regulation of DNA-templated transcription, regulation of tubulin deacetylation, response to calcium ion, response to cobalt ion, response to xenobiotic stimulus => GO:0009410, response to estrogen, response to ethanol, response to fatty acid, response to glucocorticoid, response to glucose, response to hypoxia, response to retinoic acid, response to tumor necrosis factor, skeletal muscle tissue development, somitogenesis, DNA-templated transcription, viral process InterPro: Bromodomain, Bromodomain, conserved site, CREB-binding protein/p300, atypical RING domain, Histone acetyltransferase Rtt109/CBP, Coactivator CBP, KIX domain, Nuclear receptor coactivator, ...InterPro: Bromodomain, Bromodomain, conserved site, CREB-binding protein/p300, atypical RING domain, Histone acetyltransferase Rtt109/CBP, Coactivator CBP, KIX domain, Nuclear receptor coactivator, interlocking, Nuclear receptor coactivator, CREB-bp-like, interlocking, Zinc finger, TAZ-type, Zinc finger, ZZ-type |
-Macromolecule #2: antibody 2
Macromolecule | Name: antibody 2 / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: unidentified (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris-CL, 5% glycerol, 100 mM KCl, 1 mM DTT, 0.2 mM EDTA |
Grid | Details: 200 mesh gold grid with thin carbon support |
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 2010F |
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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 | Dec 1, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 174 / 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: 30000 |
Sample stage | Specimen holder: 60 degree holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | EMAN2 |
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CTF correction | Details: per frame |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3048 |