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Yorodumi- PDB-7lvs: The CBP TAZ1 Domain in Complex with a CITED2-HIF-1-Alpha Fusion P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lvs | ||||||
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Title | The CBP TAZ1 Domain in Complex with a CITED2-HIF-1-Alpha Fusion Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION / Complex / Intrinsically Disordered Protein | ||||||
Function / homology | Function and homology information cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic process involved in female pregnancy / left/right pattern formation / pulmonary artery morphogenesis / epithelial cell differentiation involved in mammary gland alveolus development / embryonic heart tube left/right pattern formation / neural fold elevation formation / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation ...cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic process involved in female pregnancy / left/right pattern formation / pulmonary artery morphogenesis / epithelial cell differentiation involved in mammary gland alveolus development / embryonic heart tube left/right pattern formation / neural fold elevation formation / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / regulation of animal organ formation / adrenal cortex formation / TRAF6 mediated IRF7 activation / iris morphogenesis / Nuclear events mediated by NFE2L2 / nodal signaling pathway / Attenuation phase / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / embryonic camera-type eye morphogenesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / elastin metabolic process / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / glandular epithelial cell maturation / sex determination / Notch-HLH transcription pathway / regulation of transforming growth factor beta2 production / positive regulation of male gonad development / connective tissue replacement involved in inflammatory response wound healing / endocardial cushion development / determination of left/right asymmetry in lateral mesoderm / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of peroxisome proliferator activated receptor signaling pathway / hemoglobin biosynthetic process / granulocyte differentiation / lens morphogenesis in camera-type eye / retina vasculature development in camera-type eye / positive regulation of cell adhesion molecule production / germ-line stem cell population maintenance / left/right axis specification / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / collagen metabolic process / positive regulation of mitophagy / positive regulation of cell-cell adhesion / Cellular response to hypoxia / negative regulation of cardiac muscle cell proliferation / intestinal epithelial cell maturation / Regulation of lipid metabolism by PPARalpha / negative regulation of growth / regulation of protein neddylation / negative regulation of viral process / negative regulation of bone mineralization / Cytoprotection by HMOX1 / PTK6 Expression / lactate metabolic process / intracellular oxygen homeostasis / response to fluid shear stress / trophectodermal cell differentiation / B-1 B cell homeostasis / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / vascular endothelial growth factor production / outer kinetochore / peripheral nervous system development / negative regulation of interferon-beta production / negative regulation of TOR signaling / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cardiac neural crest cell development involved in heart development / transcription regulator activator activity / dopaminergic neuron differentiation / STAT3 nuclear events downstream of ALK signaling / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K27 acetyltransferase activity / positive regulation of cytokine production involved in inflammatory response / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / MRF binding / motile cilium / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / bone morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / response to iron ion / response to muscle activity / determination of left/right symmetry / face morphogenesis / negative regulation of transcription by RNA polymerase I / neural crest cell migration / embryonic hemopoiesis / positive regulation of dendritic spine development / Regulation of gene expression by Hypoxia-inducible Factor Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.02 Å | ||||||
Authors | Appling, F.D. / Berlow, R.B. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2021 Title: The molecular basis of allostery in a facilitated dissociation process. Authors: Appling, F.D. / Berlow, R.B. / Stanfield, R.L. / Dyson, H.J. / 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 | 7lvs.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lvs.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/7lvs ftp://data.pdbj.org/pub/pdb/validation_reports/lv/7lvs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11281.177 Da / Num. of mol.: 1 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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||||
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#2: Protein | Mass: 7523.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CITED2, MRG1, HIF1A, BHLHE78, MOP1, PASD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99967, UniProt: Q16665 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 6.87, 28% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.73 Å / Num. obs: 8465 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.878 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.0193→2.1458 Å / Num. unique obs: 562 / CC1/2: 0.91 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.02→40.73 Å / SU ML: 0.3266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6525 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→40.73 Å
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Refine LS restraints |
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LS refinement shell |
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