+Open data
-Basic information
Entry | Database: PDB / ID: 6dnq | ||||||
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Title | HBZ77 in complex with KIX and c-Myb | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription coactivator / transcription factor / viral / eukaryotic / complex | ||||||
Function / homology | Function and homology information positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / myeloid cell development / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production ...positive regulation of testosterone secretion / Activation of the TFAP2 (AP-2) family of transcription factors / myeloid cell development / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / positive regulation of hepatic stellate cell proliferation / Attenuation phase / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / positive regulation of hepatic stellate cell activation / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / positive regulation of transforming growth factor beta production / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / embryonic digestive tract development / stem cell division / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / myeloid cell differentiation / negative regulation of interferon-beta production / histone H3K18 acetyltransferase activity / cellular response to interleukin-6 / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / MRF binding / peroxisome proliferator activated receptor binding / face morphogenesis / negative regulation of transcription by RNA polymerase I / WD40-repeat domain binding / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of dendritic spine development / SMAD binding / behavioral response to cocaine / acetyltransferase activity / TFIIB-class transcription factor binding / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / histone acetyltransferase complex / positive regulation of collagen biosynthetic process / positive regulation of G1/S transition of mitotic cell cycle / long-term memory / histone acetyltransferase activity / positive regulation of glial cell proliferation / histone acetyltransferase / spleen development / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / viral process / B cell differentiation / thymus development / cellular response to leukemia inhibitory factor / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of smooth muscle cell proliferation / protein destabilization / protein modification process / chromatin DNA binding / cellular response to virus / PML body / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / G1/S transition of mitotic cell cycle / positive regulation of non-canonical NF-kappaB signal transduction / RNA polymerase II transcription regulator complex / calcium ion transport / cellular response to UV / disordered domain specific binding / positive regulation of neuron apoptotic process / rhythmic process / mitotic cell cycle / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / damaged DNA binding / molecular adaptor activity / transcription coactivator activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / positive regulation of gene expression / protein-containing complex binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Human T-lymphotropic virus 1 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Yang, K. / Wright, P.E. / Stanfield, R.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structural basis for cooperative regulation of KIX-mediated transcription pathways by the HTLV-1 HBZ activation domain. Authors: Yang, K. / Stanfield, R.L. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dnq.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dnq.ent.gz | 93.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dnq_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
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Full document | 6dnq_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 6dnq_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6dnq_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/6dnq ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dnq | HTTPS FTP |
-Related structure data
Related structure data | 6dmxC 2aghS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 8728.772 Da / Num. of mol.: 1 / Fragment: residues 3-77 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: HBZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q2Q067 | ||||||
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#2: Protein/peptide | Mass: 3810.263 Da / Num. of mol.: 2 / Fragment: residues 284-315 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myb / Production host: Escherichia coli (E. coli) / References: UniProt: P06876 #3: Protein | Mass: 10485.053 Da / Num. of mol.: 2 / Fragment: residues 586-672 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli) / References: UniProt: P45481, histone acetyltransferase #4: Chemical | ChemComp-EDO / | #5: 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: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 14320 / % possible obs: 97.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 38 Å2 / CC1/2: 0.87 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.35→2.39 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AGH Resolution: 2.35→36.019 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→36.019 Å
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Refine LS restraints |
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LS refinement shell |
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