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- EMDB-6263: p300 binding with antibody 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-6263
Titlep300 binding with antibody 2
Map datap300 bound to antibody 2
Sample
  • Sample: p300 bound to antibody 2
  • Protein or peptide: histone acetyltransferase p300
  • Protein or peptide: antibody 2
KeywordsP300 / Estrogen Receptor
Function / homology
Function and homology information


core promoter sequence-specific DNA binding => GO:0001046 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / DNA-binding transcription factor binding => GO:0140297 / nuclear receptor binding => GO:0016922 / : / : / response to xenobiotic stimulus => GO:0009410 / : / : ...core promoter sequence-specific DNA binding => GO:0001046 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / : / DNA-binding transcription factor binding => GO:0140297 / nuclear receptor binding => GO:0016922 / : / : / response to xenobiotic stimulus => GO:0009410 / : / : / positive regulation of sarcomere organization / protein binding / positive regulation of glycoprotein biosynthetic process / protein-DNA complex assembly / behavioral defense response / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / peptide butyryltransferase activity / histone H2B acetyltransferase activity / thigmotaxis / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / regulation of angiotensin metabolic process / protein propionyltransferase activity / NOTCH2 intracellular domain regulates transcription / peptidyl-lysine acetylation / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / histone H3K122 acetyltransferase activity / response to fatty acid / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / cellular response to L-leucine / histone H3 acetyltransferase activity / response to cobalt ion / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / STAT3 nuclear events downstream of ALK signaling / N-terminal peptidyl-lysine acetylation / NFE2L2 regulates pentose phosphate pathway genes / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / TGFBR3 expression / digestive tract development / positive regulation by host of viral transcription / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / histone H3K27 acetyltransferase activity / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / histone H3K18 acetyltransferase activity / Nuclear events mediated by NFE2L2 / face morphogenesis / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / NOTCH3 Intracellular Domain Regulates Transcription / platelet formation / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / megakaryocyte development / NFE2L2 regulating anti-oxidant/detoxification enzymes / positive regulation of DNA binding / regulation of tubulin deacetylation / STAT family protein binding / protein-lysine-acetyltransferase activity / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / internal protein amino acid acetylation / transcription factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / fat cell differentiation / PI5P Regulates TP53 Acetylation / acetyltransferase activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / positive regulation of proteolysis / RUNX3 regulates p14-ARF / positive regulation of cell size / : / response to tumor necrosis factor / positive regulation of collagen biosynthetic process / histone acetyltransferase complex / NF-kappaB binding / positive regulation of type I interferon production / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
Similarity search - Function
Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP ...Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone acetyltransferase p300
Similarity search - Component
Biological speciesHomo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 32.0 Å
AuthorsYi P / Wang Z / Feng Q / Pintilie GD / Foulds CE / Lanz RB / Ludtke SJ / Schmid MF / Chiu W / O'Malley BW
CitationJournal: 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
DepositionFeb 2, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseAug 26, 2015-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6263.gif

Downloads & links

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Map

FileDownload / File: emd_6263.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp300 bound to antibody 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 200 pix.
= 432. Å		2.16 Å/pix.
x 200 pix.
= 432. Å		2.16 Å/pix.
x 200 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 4.0 / Movie #1: 4.2
Minimum - Maximum-5.17813921 - 13.523746490000001
Average (Standard dev.)0.17908418 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-114-89
Dimensions200200200
Spacing200200200
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.162.162.16
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-114-96-89
NC/NR/NS200200200
D min/max/mean-5.17813.5240.179

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Supplemental data

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Sample components

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Entire : p300 bound to antibody 2

EntireName: p300 bound to antibody 2
Components
  • Sample: p300 bound to antibody 2
  • Protein or peptide: histone acetyltransferase p300
  • Protein or peptide: antibody 2

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Supramolecule #1000: p300 bound to antibody 2

SupramoleculeName: p300 bound to antibody 2 / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa

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Macromolecule #1: histone acetyltransferase p300

MacromoleculeName: histone acetyltransferase p300 / type: protein_or_peptide / ID: 1 / Name.synonym: EP300 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 300 KDa / Theoretical: 300 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9
SequenceUniProtKB: 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, L-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, GO: 0071407, 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

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Macromolecule #2: antibody 2

MacromoleculeName: antibody 2 / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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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

Concentration0.1 mg/mL
BufferpH: 8
Details: 20 mM Tris-CL, 5% glycerol, 100 mM KCl, 1 mM DTT, 0.2 mM EDTA
GridDetails: 200 mesh gold grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1 second before plunging.

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 90 K / Max: 105 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateDec 1, 2012
Image recordingCategory: 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 min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder: 60 degree holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsEMAN2
CTF correctionDetails: per frame
Final reconstructionResolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3048

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