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Open data
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Basic information
Entry | Database: PDB / ID: 8beb | ||||||
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Title | Ternary complex between VCB, BRD4-BD1 and PROTAC 49 | ||||||
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![]() | LIGASE / PROTAC / degrader / complex / E3 ligase / VHL / VCB | ||||||
Function / homology | ![]() regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II C-terminal domain binding / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of DNA damage checkpoint / P-TEFb complex binding / ubiquitin-like ligase-substrate adaptor activity / negative regulation by host of viral transcription / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / positive regulation of T-helper 17 cell lineage commitment / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / negative regulation of autophagy / RNA polymerase II CTD heptapeptide repeat kinase activity / transcription corepressor binding / condensed nuclear chromosome / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Vif-mediated degradation of APOBEC3G / lysine-acetylated histone binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cell morphogenesis / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromosome / Neddylation / Replication of the SARS-CoV-2 genome / regulation of inflammatory response / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / amyloid fibril formation / Potential therapeutics for SARS / molecular adaptor activity / transcription coactivator activity / protein stabilization / transcription cis-regulatory region binding / protein ubiquitination / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / DNA damage response / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sorrell, F.J. / Mueller, J.E. / Lehmann, M. / Wegener, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design. Authors: Krieger, J. / Sorrell, F.J. / Wegener, A.A. / Leuthner, B. / Machrouhi-Porcher, F. / Hecht, M. / Leibrock, E.M. / Muller, J.E. / Eisert, J. / Hartung, I.V. / Schlesiger, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200.4 KB | Display | ![]() |
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PDB format | ![]() | 157.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.1 KB | Display | ![]() |
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Full document | ![]() | 803.9 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bdiC ![]() 8bdjC ![]() 8bdlC ![]() 8bdmC ![]() 8bdnC ![]() 8bdoC ![]() 8bdsC ![]() 8bdtC ![]() 8bdxC ![]() 3mxfS ![]() 5nw1S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 4 types, 4 molecules ABCD
#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: 18702.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 15099.380 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 3 types, 5 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/QIK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QIK.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-SO4 / |
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#6: Chemical | ChemComp-QIK / ( |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.8M ammonium sulfate, 4% (w/v) glycerol, 0.1M bis-Tris pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→64.7 Å / Num. obs: 9832 / % possible obs: 85.4 % / Redundancy: 18.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.353 / Rpim(I) all: 0.084 / Rrim(I) all: 0.363 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 3.18→3.346 Å / Redundancy: 20.9 % / Rmerge(I) obs: 2.206 / Num. unique obs: 493 / CC1/2: 0.512 / Rpim(I) all: 0.492 / Rrim(I) all: 2.261 / % possible all: 41.2 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5nw1, 3mxf Resolution: 3.18→64.7 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.881 / SU B: 61.758 / SU ML: 0.447 / SU R Cruickshank DPI: 0.4791 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.593 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.5 Å2 / Biso mean: 71.841 Å2 / Biso min: 8.96 Å2
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Refinement step | Cycle: final / Resolution: 3.18→64.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.18→3.262 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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