+Open data
-Basic information
Entry | Database: PDB / ID: 3cbp | ||||||
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Title | Set7/9-ER-Sinefungin complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE RECEPTOR / Estrogen Receptor / protein lysine methylation / Activator / Chromatin regulator / Chromosomal protein / Methyltransferase / Nucleus / S-adenosyl-L-methionine / Transcription / Transcription regulation / Transferase / DNA-binding / Lipid-binding / Metal-binding / Phosphoprotein / Steroid-binding / Zinc-finger / TRANSFERASE-TRANSFERASE RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity ...heterochromatin organization / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / histone methyltransferase activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / negative regulation of miRNA transcription / protein localization to chromatin / 14-3-3 protein binding / cellular response to estradiol stimulus / transcription coregulator binding / nitric-oxide synthase regulator activity / steroid binding / TBP-class protein binding / ESR-mediated signaling / transcription corepressor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / PKMTs methylate histone lysines / Nuclear Receptor transcription pathway / euchromatin / negative regulation of DNA-binding transcription factor activity / p53 binding / Constitutive Signaling by Aberrant PI3K in Cancer / transcription coactivator binding / nuclear receptor activity / beta-catenin binding / positive regulation of fibroblast proliferation / response to estrogen / chromosome / Regulation of RUNX2 expression and activity / male gonad development / PIP3 activates AKT signaling / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / regulation of inflammatory response / chromatin organization / response to estradiol / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / transcription regulator complex / response to ethanol / Estrogen-dependent gene expression / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Cheng, X. / Jia, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase. Authors: Subramanian, K. / Jia, D. / Kapoor-Vazirani, P. / Powell, D.R. / Collins, R.E. / Sharma, D. / Peng, J. / Cheng, X. / Vertino, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cbp.cif.gz | 68 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cbp.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cbp_validation.pdf.gz | 827.5 KB | Display | wwPDB validaton report |
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Full document | 3cbp_full_validation.pdf.gz | 832.4 KB | Display | |
Data in XML | 3cbp_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 3cbp_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/3cbp ftp://data.pdbj.org/pub/pdb/validation_reports/cb/3cbp | HTTPS FTP |
-Related structure data
Related structure data | 3cbmC 3cboC 1o9sS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 28563.785 Da / Num. of mol.: 1 / Fragment: UNP residues 111-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SETD7, KIAA1717, KMT7, SET7, SET9 / Plasmid: pXC408 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C+ / Keywords: catalytic domain References: UniProt: Q8WTS6, histone-lysine N-methyltransferase |
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#2: Protein/peptide | Mass: 1148.400 Da / Num. of mol.: 1 / Fragment: UNP residues 298-307 / Source method: obtained synthetically / Details: ER peptide / Keywords: ER peptid / References: UniProt: P03372 |
-Non-polymers , 4 types, 122 molecules
#3: Chemical | ChemComp-SFG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.38 % |
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Crystal grow | pH: 8 Details: 40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→23.82 Å / Num. obs: 48755 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.42→1.47 Å / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 3 / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1O9S Resolution: 1.42→23.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 806155.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: BULK SOLVENT MODELING. METHOD USED : FLAT MODEL KSOL : 0.464112 BSOL : 54.7698 (A**2)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.7698 Å2 / ksol: 0.464112 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.42→23.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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