+Open data
-Basic information
Entry | Database: PDB / ID: 8hog | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Bcl-2 in complex with sonrotoclax | ||||||
Components | Apoptosis regulator Bcl-2 | ||||||
Keywords | APOPTOSIS / Inhibitor | ||||||
Function / homology | Chem-98I Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, J. / Xu, M. / Feng, Y. / Hong, Y. / Liu, Y. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Blood / Year: 2024 Title: Sonrotoclax overcomes BCL2 G101V mutation-induced venetoclax resistance in preclinical models of hematologic malignancy. Authors: Liu, J. / Li, S. / Wang, Q. / Feng, Y. / Xing, H. / Yang, X. / Guo, Y. / Guo, Y. / Sun, H. / Liu, X. / Yang, S. / Mei, Z. / Zhu, Y. / Cheng, Z. / Chen, S. / Xu, M. / Zhang, W. / Wan, N. / ...Authors: Liu, J. / Li, S. / Wang, Q. / Feng, Y. / Xing, H. / Yang, X. / Guo, Y. / Guo, Y. / Sun, H. / Liu, X. / Yang, S. / Mei, Z. / Zhu, Y. / Cheng, Z. / Chen, S. / Xu, M. / Zhang, W. / Wan, N. / Wang, J. / Ma, Y. / Zhang, S. / Luan, X. / Xu, A. / Li, L. / Wang, H. / Yang, X. / Hong, Y. / Xue, H. / Yuan, X. / Hu, N. / Song, X. / Wang, Z. / Liu, X. / Wang, L. / Liu, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hog.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hog.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 8hog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hog_validation.pdf.gz | 751.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8hog_full_validation.pdf.gz | 752.7 KB | Display | |
Data in XML | 8hog_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8hog_validation.cif.gz | 10.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8hog ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8hog | HTTPS FTP |
-Related structure data
Related structure data | 8hohC 8hoiC 5vauS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18976.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
---|---|
#2: Chemical | ChemComp-98I / ~{ |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.34 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-tris propane pH 9.0, 30% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.54 Å / Num. obs: 15163 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 30.52 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.533 / Num. unique obs: 1467 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VAU Resolution: 1.8→50.54 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.51 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.25 Å2 / Biso mean: 44.5792 Å2 / Biso min: 22.43 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→50.54 Å
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %
|