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- PDB-6gfx: pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide conta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gfx | |||||||||
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Title | pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 13a) | |||||||||
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![]() | LIGASE / PROTEIN-PEPTIDE COMPLEX / UBIQUITIN LIGASE / HYPOXIA INDUCIBLE FACTOR | |||||||||
Function / homology | ![]() epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / glandular epithelial cell maturation / elastin metabolic process / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / glandular epithelial cell maturation / elastin metabolic process / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / retina vasculature development in camera-type eye / Cellular response to hypoxia / intestinal epithelial cell maturation / positive regulation of mitophagy / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / regulation of cellular response to hypoxia / negative regulation of bone mineralization / intracellular oxygen homeostasis / B-1 B cell homeostasis / vascular endothelial growth factor production / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription regulator activator activity / transcription elongation factor activity / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / target-directed miRNA degradation / dopaminergic neuron differentiation / lactate metabolic process / elongin complex / VCB complex / STAT3 nuclear events downstream of ALK signaling / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of TOR signaling / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / Replication of the SARS-CoV-1 genome / response to iron ion / response to muscle activity / neural crest cell migration / Cul5-RING ubiquitin ligase complex / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / DNA-binding transcription repressor activity / PTK6 promotes HIF1A stabilization / DNA-binding transcription activator activity / digestive tract morphogenesis / regulation of aerobic respiration / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / SUMOylation of ubiquitinylation proteins / positive regulation of epithelial cell migration / axonal transport of mitochondrion / bone mineralization / heart looping / outflow tract morphogenesis / negative regulation of transcription elongation by RNA polymerase II / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / TOR signaling / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / Tat-mediated elongation of the HIV-1 transcript / epithelial to mesenchymal transition / Formation of HIV-1 elongation complex containing HIV-1 Tat / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of chemokine production / axon cytoplasm / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Castro, G.V. / Testa, A. / Ciulli, A. | |||||||||
Funding support | 1items
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![]() | ![]() Title: 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. Authors: Testa, A. / Lucas, X. / Castro, G.V. / Chan, K.H. / Wright, J.E. / Runcie, A.C. / Gadd, M.S. / Harrison, W.T.A. / Ko, E.J. / Fletcher, D. / Ciulli, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.3 KB | Display | ![]() |
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PDB format | ![]() | 125.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 11748.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10974.616 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 18558.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein/peptide | Mass: 2278.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20-22% PEG MME 5000, 0.2 M ammonium sulfate, 0.1 M potassium phosphate, 10 mM DTT PH range: 6.0 - 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→61.33 Å / Num. obs: 39987 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.024 / Rrim(I) all: 0.098 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.83→1.87 Å / Redundancy: 15.2 % / Rmerge(I) obs: 1.083 / Num. unique obs: 2427 / CC1/2: 0.87 / Rpim(I) all: 0.286 / Rrim(I) all: 1.121 / % possible all: 99.9 |
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Processing
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Refinement | Resolution: 1.83→61.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.574 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.113 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.12 Å2 / Biso mean: 31.778 Å2 / Biso min: 12.13 Å2
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Refinement step | Cycle: final / Resolution: 1.83→61.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.877 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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