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- PDB-8hoi: Crystal structure of Bcl-2 D103Y in complex with sonrotoclax -

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Basic information

Entry
Database: PDB / ID: 8hoi
TitleCrystal structure of Bcl-2 D103Y in complex with sonrotoclax
ComponentsApoptosis regulator Bcl-2
KeywordsAPOPTOSIS / Inhibitor
Function / homologyChem-98I / FORMIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
B: Apoptosis regulator Bcl-2
C: Apoptosis regulator Bcl-2
D: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7039
Polymers76,0974
Non-polymers3,6065
Water3,693205
1
A: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9142
Polymers19,0241
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9603
Polymers19,0241
Non-polymers9362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9142
Polymers19,0241
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Apoptosis regulator Bcl-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9142
Polymers19,0241
Non-polymers8901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.367, 86.737, 73.395
Angle α, β, γ (deg.)90.000, 105.020, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Apoptosis regulator Bcl-2


Mass: 19024.170 Da / Num. of mol.: 4 / Mutation: D103Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / 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.: 4 / Source method: obtained synthetically / Formula: C49H59N7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.96 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Acetate pH 5.1, 3.6 M Sodium Formate, 0.1 M Lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.34 Å / Num. obs: 40244 / % possible obs: 95.4 % / Redundancy: 7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.055 / Rrim(I) all: 0.147 / Net I/σ(I): 9.8 / Num. measured all: 281401 / Scaling rejects: 7
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.714 / Num. unique obs: 3751 / CC1/2: 0.823 / Rpim(I) all: 0.288 / Rrim(I) all: 0.771 / % possible all: 96.4

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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: 2.25→39.71 Å / Cross valid method: THROUGHOUT / σ(F): 38.73 / Phase error: 34.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2643 2001 5.2 %
Rwork0.2359 38226 -
obs0.2416 40227 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.72 Å2 / Biso mean: 30.6553 Å2 / Biso min: 15.98 Å2
Refinement stepCycle: final / Resolution: 2.25→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 259 205 5056
Biso mean--26.13 33.47 -
Num. residues----547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.32091460.30742757290391
2.31-2.370.34561450.29192775292091
2.37-2.440.30171410.29052718285992
2.44-2.520.35671450.29152712285790
2.52-2.610.33471370.28942606274387
2.61-2.710.2961480.27782823297192
2.71-2.830.28171400.26992758289892
2.83-2.980.27671450.25562765291092
2.98-3.170.25391370.24592594273187
3.17-3.420.24311440.23772795293993
3.42-3.760.24171460.21472790293692
3.76-4.30.21241370.19772635277287
4.3-5.420.25141500.19222799294992
5.42-39.710.27321400.24332699283987
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.356-1.76050.42073.0688-1.48381.2367-0.3777-0.51630.3320.5538-0.04050.2482-0.1163-0.0980.21090.38790.00690.03070.4833-0.13070.307938.5894-17.197266.5733
21.69730.45370.04390.663-0.21690.3725-0.09980.09880.31990.15150.0605-0.2166-0.1190.0650.01330.2510.037-0.09890.2643-0.02940.302946.0872-26.131452.8814
31.72820.0335-0.36011.12520.15880.77840.1458-0.0645-0.12110.2113-0.068-0.05490.17680.1599-0.04490.24670.0168-0.11210.3022-0.00810.259947.38-30.682160.9169
42.07881.15170.27863.11250.52250.6084-0.00360.42560.1183-0.4485-0.11130.1883-0.00820.22730.10670.29720.0264-0.04220.44980.05030.212411.0641-21.076647.2178
51.10350.01440.65770.6082-0.01221.4394-0.03430.08590.3885-0.0342-0.1530.2088-0.0715-0.08110.12380.23040.04-0.17640.2473-0.01390.4571.6057-21.590658.6025
61.7859-0.37470.82180.44050.2490.99690.2453-0.3571-0.2043-0.2044-0.21730.2160.0146-0.2413-0.02680.1889-0.0189-0.090.27430.00390.221912.2362-34.242161.4081
71.4197-0.1062-0.3791.0521-0.17540.42690.09840.0322-0.0987-0.1463-0.06520.06780.0208-0.0545-0.02220.25950.0069-0.04830.27860.00560.20619.888-30.545852.6015
81.91920.2547-0.78471.86961.01751.19440.14180.28880.4909-0.5529-0.05390.1725-0.1743-0.39160.07980.201-0-0.18730.6181-0.07340.2501-6.7679-27.805845.8624
90.4296-0.2192-0.30732.28050.94242.4105-0.05560.26450.1096-0.0373-0.3146-0.30640.37240.32980.21980.2640.0292-0.03290.63750.14070.27232.2041-5.963433.6324
101.88521.53640.93491.32780.99541.25050.28920.1301-0.24180.2870.0948-0.38440.57790.1644-0.34210.69370.1586-0.11010.42180.07310.662933.8679-10.988330.2071
110.85750.03540.71081.3417-0.19412.89060.1806-0.1699-0.234-0.0093-0.1047-0.1680.381-0.1142-0.03880.2184-0.05580.00060.24060.02220.247218.832-6.871637.6957
121.20120.5917-0.11860.7746-0.67671.8874-0.0484-0.4108-0.2757-0.28330.01750.0584-0.068-0.2740.02450.151-0.0171-0.06540.29370.03530.246919.50844.225523.0501
131.1498-0.2829-0.64171.34030.22321.7467-0.10030.0848-0.0001-0.059-0.068-0.06020.04160.12250.05860.22330.0029-0.04110.34240.02160.168625.52921.462329.7475
141.68-0.10531.5152-0.0002-0.09171.35550.0381-0.05850.35360.24610.0885-0.4261-0.25480.43730.01750.4619-0.2044-0.2310.69630.10150.011930.519810.383944.2163
151.50550.8003-0.02111.78570.63530.3419-0.2944-0.21930.05350.2507-0.2592-0.51990.06940.36730.1531-0.3345-0.101-0.4040.85890.02160.058229.2128-0.768349.1264
160.66990.7089-0.13934.5881-2.12854.2201-0.0064-0.17690.206-0.134-0.14990.36810.3754-0.54680.10430.2312-0.05970.03180.5086-0.12490.32053.2918-7.043966.9571
173.0357-0.2247-0.49971.30260.13111.2977-0.1934-0.2093-0.07720.1665-0.02480.17770.1996-0.370.14110.2872-0.0216-0.03550.3536-0.02670.191912.6506-7.31156.7648
181.1919-0.2973-0.80120.78640.39912.626-0.04850.1082-0.13250.0692-0.0748-0.08090.07060.49680.10680.166-0.0107-0.05040.323-0.01770.234619.71950.51672.8188
190.88290.0923-0.76380.81780.36991.6684-0.03610.11650.0277-0.0526-0.15760.1332-0.167-0.21020.09170.18510.0195-0.05740.3471-0.01220.21029.91562.725563.8607
202.8885-1.2650.82984.9259-0.66661.02970.0653-0.43850.29330.3679-0.06630.02270.0293-0.2959-0.00880.28450.01-0.03810.3994-0.10320.310444.3054-21.958365.3964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 27 through 91 )C27 - 91
2X-RAY DIFFRACTION2chain 'C' and (resid 92 through 137 )C92 - 137
3X-RAY DIFFRACTION3chain 'C' and (resid 138 through 204 )C138 - 204
4X-RAY DIFFRACTION4chain 'D' and (resid 10 through 91 )D10 - 91
5X-RAY DIFFRACTION5chain 'D' and (resid 92 through 117 )D92 - 117
6X-RAY DIFFRACTION6chain 'D' and (resid 118 through 143 )D118 - 143
7X-RAY DIFFRACTION7chain 'D' and (resid 144 through 193 )D144 - 193
8X-RAY DIFFRACTION8chain 'D' and (resid 194 through 204 )D194 - 204
9X-RAY DIFFRACTION9chain 'A' and (resid 9 through 26 )A9 - 26
10X-RAY DIFFRACTION10chain 'A' and (resid 27 through 91 )A27 - 91
11X-RAY DIFFRACTION11chain 'A' and (resid 92 through 117 )A92 - 117
12X-RAY DIFFRACTION12chain 'A' and (resid 118 through 137 )A118 - 137
13X-RAY DIFFRACTION13chain 'A' and (resid 138 through 184 )A138 - 184
14X-RAY DIFFRACTION14chain 'A' and (resid 185 through 193 )A185 - 193
15X-RAY DIFFRACTION15chain 'A' and (resid 194 through 204 )A194 - 204
16X-RAY DIFFRACTION16chain 'B' and (resid 10 through 91 )B10 - 91
17X-RAY DIFFRACTION17chain 'B' and (resid 92 through 107 )B92 - 107
18X-RAY DIFFRACTION18chain 'B' and (resid 108 through 137 )B108 - 137
19X-RAY DIFFRACTION19chain 'B' and (resid 138 through 204 )B138 - 204
20X-RAY DIFFRACTION20chain 'C' and (resid 10 through 26 )C10 - 26

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