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- PDB-8hog: Crystal structure of Bcl-2 in complex with sonrotoclax -

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Basic information

Entry
Database: PDB / ID: 8hog
TitleCrystal structure of Bcl-2 in complex with sonrotoclax
ComponentsApoptosis regulator Bcl-2
KeywordsAPOPTOSIS / Inhibitor
Function / homologyChem-98I
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, J. / Xu, M. / Feng, Y. / Hong, Y. / Liu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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
DepositionDec 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8662
Polymers18,9761
Non-polymers8901
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.560, 47.549, 101.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apoptosis regulator Bcl-2


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 / ~{N}-[4-[(4-methyl-4-oxidanyl-cyclohexyl)methylamino]-3-nitro-phenyl]sulfonyl-4-[2-[(2~{S})-2-(2-propan-2-ylphenyl)pyrrolidin-1-yl]-7-azaspiro[3.5]nonan-7-yl]-2-(1~{H}-pyrrolo[2,3-b]pyridin-5-yloxy)benzamide


Mass: 890.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H59N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-tris propane pH 9.0, 30% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.8→1.84 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.533 / Num. unique obs: 1467 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAU

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
RfactorNum. reflection% reflection
Rfree0.238 723 4.77 %
Rwork0.2164 14424 -
obs0.2175 15147 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 44.5792 Å2 / Biso min: 22.43 Å2
Refinement stepCycle: final / Resolution: 1.8→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 64 54 1316
Biso mean--36.16 45.68 -
Num. residues----144
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.940.33591450.277927992944
1.94-2.130.29461360.237228522988
2.13-2.440.27281520.22528452997
2.44-3.080.27371400.239528913031
3.08-50.540.1991500.19730373187

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