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- PDB-8hoh: Crystal structure of Bcl-2 G101V in complex with sonrotoclax -

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Basic information

Entry
Database: PDB / ID: 8hoh
TitleCrystal structure of Bcl-2 G101V 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: 1.9 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)19,9082
Polymers19,0181
Non-polymers8901
Water1,20767
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)32.479, 48.036, 106.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19018.162 Da / Num. of mol.: 1 / Mutation: G101V
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: isolated from a natural source / Formula: C49H59N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris hydrochloride pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→53.21 Å / Num. obs: 13776 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 26.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.119 / Net I/σ(I): 14.7 / Num. measured all: 168729 / Scaling rejects: 66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.9412.80.663112068730.9450.1930.6913.799.9
9.11-53.219.10.06814921640.9980.0240.07225.198.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAU

5vau


Resolution: 1.9→43.78 Å / SU ML: 0.2759 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4719
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2571 650 4.74 %
Rwork0.2271 13067 -
obs0.2286 13717 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1153 0 64 67 1284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071256
X-RAY DIFFRACTIONf_angle_d0.88251710
X-RAY DIFFRACTIONf_chiral_restr0.0568170
X-RAY DIFFRACTIONf_plane_restr0.0062248
X-RAY DIFFRACTIONf_dihedral_angle_d15.2343486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.050.39841260.29442550X-RAY DIFFRACTION99.18
2.05-2.250.29521200.23922556X-RAY DIFFRACTION99.7
2.25-2.580.27881270.24052592X-RAY DIFFRACTION99.63
2.58-3.250.26941280.23192632X-RAY DIFFRACTION99.86
3.25-43.780.21921490.20762737X-RAY DIFFRACTION99.9

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