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Yorodumi- PDB-7jtp: Crystal structure of Protac MS67 in complex with the WD repeat-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jtp | ||||||
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Title | Crystal structure of Protac MS67 in complex with the WD repeat-containing protein 5 and pVHL:ElonginC:ElonginB | ||||||
Components |
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Keywords | PROTEIN BINDING / Protac / protein degradation / ubiquitination | ||||||
Function / homology | Function and homology information 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 / MLL3/4 complex / elongin complex / Set1C/COMPASS complex / VCB complex / MLL1/2 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 / MLL3/4 complex / elongin complex / Set1C/COMPASS complex / VCB complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Replication of the SARS-CoV-1 genome / Cardiogenesis / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / histone methyltransferase complex / regulation of tubulin deacetylation / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / regulation of embryonic development / MLL1 complex / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / histone acetyltransferase complex / 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 / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / positive regulation of gluconeogenesis / negative regulation of TORC1 signaling / transcription initiation-coupled chromatin remodeling / methylated histone binding / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / transcription corepressor binding / skeletal system development / gluconeogenesis / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Regulation of expression of SLITs and ROBOs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / Replication of the SARS-CoV-2 genome / HATs acetylate histones / histone binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / protein stabilization / molecular adaptor activity / protein ubiquitination / regulation of cell cycle / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Kottur, J. / Jain, R. / Aggarwal, A.K. | ||||||
Citation | Journal: Sci Transl Med / Year: 2021 Title: A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models. Authors: Yu, X. / Li, D. / Kottur, J. / Shen, Y. / Kim, H.S. / Park, K.S. / Tsai, Y.H. / Gong, W. / Wang, J. / Suzuki, K. / Parker, J. / Herring, L. / Kaniskan, H.U. / Cai, L. / Jain, R. / Liu, J. / ...Authors: Yu, X. / Li, D. / Kottur, J. / Shen, Y. / Kim, H.S. / Park, K.S. / Tsai, Y.H. / Gong, W. / Wang, J. / Suzuki, K. / Parker, J. / Herring, L. / Kaniskan, H.U. / Cai, L. / Jain, R. / Liu, J. / Aggarwal, A.K. / Wang, G.G. / Jin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jtp.cif.gz | 156.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jtp.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jtp ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jtp | HTTPS FTP |
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-Related structure data
Related structure data | 7jtoC 1vcbS 2gnqS 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
-Protein , 4 types, 4 molecules JKLA
#1: Protein | Mass: 11748.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Plasmid: pCDF Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370 |
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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.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: pCDF Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369 |
#3: Protein | Mass: 18702.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337 |
#4: Protein | Mass: 34037.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61964 |
-Non-polymers , 3 types, 443 molecules
#5: Chemical | ChemComp-GOL / |
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#6: Chemical | ChemComp-X6M / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, pH 8.5, 30% PEG300 / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→78.033 Å / Num. all: 46516 / Num. obs: 46516 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.02 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Rsym value: 0.095 / Net I/av σ(I): 4.7 / Net I/σ(I): 11.7 / Num. measured all: 331442 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2GNQ & 1VCB Resolution: 2.12→57.089 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML
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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 max: 93.47 Å2 / Biso mean: 40.2234 Å2 / Biso min: 16.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.12→57.089 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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