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- PDB-5svh: Crystal structure of the KIX domain of CBP in complex with a MLL/... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5svh | ||||||
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Title | Crystal structure of the KIX domain of CBP in complex with a MLL/c-Myb chimera | ||||||
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![]() | TRANSCRIPTION / CBP / complex | ||||||
Function / homology | ![]() protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / negative regulation of DNA methylation-dependent heterochromatin formation / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / negative regulation of DNA methylation-dependent heterochromatin formation / 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 / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / regulation of smoothened signaling pathway / histone H3K18 acetyltransferase activity / 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 / definitive hemopoiesis / NFE2L2 regulating MDR associated enzymes / MRF binding / histone H3K4 methyltransferase activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / 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 / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / embryonic hemopoiesis / Regulation of NFE2L2 gene expression / exploration behavior / anterior/posterior pattern specification / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / NFE2L2 regulating anti-oxidant/detoxification enzymes / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / peptide-lysine-N-acetyltransferase activity / FOXO-mediated transcription of cell death genes / histone methyltransferase complex / embryonic digit morphogenesis / homeostatic process / protein acetylation / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / acetyltransferase activity / stimulatory C-type lectin receptor signaling pathway / Zygotic genome activation (ZGA) / minor groove of adenine-thymine-rich DNA binding / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / membrane depolarization / MLL1 complex / histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / Transcriptional and post-translational regulation of MITF-M expression and activity / Attenuation phase / cellular response to nutrient levels / canonical NF-kappaB signal transduction / regulation of cellular response to heat / negative regulation of fibroblast proliferation / histone acetyltransferase activity / histone acetyltransferase / homeostasis of number of cells within a tissue / spleen development / cellular response to transforming growth factor beta stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RORA activates gene expression / NPAS4 regulates expression of target genes / Regulation of lipid metabolism by PPARalpha / CD209 (DC-SIGN) signaling / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / post-embryonic development / circadian regulation of gene expression / lysine-acetylated histone binding / Formation of the beta-catenin:TCF transactivating complex / Heme signaling / protein destabilization / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein modification process / visual learning / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Evasion by RSV of host interferon responses / chromatin DNA binding / NOTCH1 Intracellular Domain Regulates Transcription / PKMTs methylate histone lysines / transcription coactivator binding / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Langelaan, D.N. / Smith, S.P. / Allingham, J.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design of a nanomolar affinity ligand to the KIX domain of CBP Authors: Langelaan, D.N. / Smith, S.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.3 KB | Display | ![]() |
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PDB format | ![]() | 30 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2aghS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 10353.856 Da / Num. of mol.: 1 / Fragment: UNP residues 587-673 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 6383.193 Da / Num. of mol.: 1 Fragment: UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315,UNP Q03164 residues 2839-2869 linked to UNP P01103 residues 291-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1, MYB / Production host: ![]() ![]() References: UniProt: Q03164, UniProt: P01103, histone-lysine N-methyltransferase | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.6 % / Description: Large hexagonal prism |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1 M potassium sulfate 2.3M Ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→59.9 Å / Num. obs: 13648 / % possible obs: 98.7 % / Redundancy: 27.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.05→2.123 Å / Redundancy: 24.7 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.871 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2agh Resolution: 2.05→59.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→59.9 Å
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Refine LS restraints |
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LS refinement shell |
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