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- PDB-8srx: Crystal structure of BAK-BAX heterodimer with lysoPC -

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Basic information

Entry
Database: PDB / ID: 8srx
TitleCrystal structure of BAK-BAX heterodimer with lysoPC
Components
  • Apoptosis regulator BAX
  • Bcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / BAX / BAK / BCL2
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / spermatid differentiation / Activation and oligomerization of BAK protein / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / BH domain binding / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell homeostatic proliferation / B cell negative selection / BAK complex / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / apoptotic process involved in embryonic digit morphogenesis / mitochondrial fragmentation involved in apoptotic process / response to mycotoxin / mitochondrial permeability transition pore complex / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / epithelial cell apoptotic process / motor neuron apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / execution phase of apoptosis / porin activity / thymocyte apoptotic process / pore complex / hypothalamus development / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / apoptotic mitochondrial changes / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / germ cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / BH3 domain binding / positive regulation of calcium ion transport into cytosol / negative regulation of mitochondrial membrane potential / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of apoptotic signaling pathway / blood vessel remodeling / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / ectopic germ cell programmed cell death / response to axon injury / ovarian follicle development / negative regulation of fibroblast proliferation / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway / negative regulation of protein binding / heat shock protein binding / response to salt stress / extrinsic apoptotic signaling pathway in absence of ligand / release of sequestered calcium ion into cytosol / homeostasis of number of cells within a tissue / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria
Similarity search - Function
Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 ...Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-K6G / DI(HYDROXYETHYL)ETHER / Apoptosis regulator BAX / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBrouwer, J.M. / Czabotar, P.E. / Colman, P.M. / Miller, M.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Febs J. / Year: 2024
Title: Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids.
Authors: Miller, M.S. / Cowan, A.D. / Brouwer, J.M. / Smyth, S.T. / Peng, L. / Wardak, A.Z. / Uren, R.T. / Luo, C. / Roy, M.J. / Shah, S. / Tan, Z. / Reid, G.E. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Apoptosis regulator BAX
C: Bcl-2 homologous antagonist/killer
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,27715
Polymers37,3044
Non-polymers1,97311
Water2,054114
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)158.166, 45.562, 43.714
Angle α, β, γ (deg.)90.00, 101.76, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-324-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 9832.919 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Protein Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 8819.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812

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Non-polymers , 7 types, 125 molecules

#3: Chemical ChemComp-K6G / [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate


Mass: 496.638 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H51NO7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 0.1 M Bis-tris chloride pH 5.5, 25% PEG 3350, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.09→38.71 Å / Num. obs: 18140 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.198 / Rrim(I) all: 0.216 / Net I/σ(I): 8.62
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.09-2.151.55712830.3991.7011
2.15-2.211.25412990.4941.3691
2.21-2.271.00112830.6281.0921
2.27-2.340.9312300.7171.0151
2.34-2.420.72911920.7790.7951
2.42-2.50.75711370.7830.8251
2.5-2.60.5811030.8620.6321
2.6-2.70.45910700.930.51
2.7-2.820.37410390.9340.4071
2.82-2.960.2969860.960.3231
2.96-3.120.2169380.9790.2351
3.12-3.310.1678960.9870.1821
3.31-3.540.1188340.9940.1281
3.54-3.820.0877760.9950.0951
3.82-4.190.0767270.9960.0831
4.19-4.680.0676550.9970.0731
4.68-5.410.075820.9970.0761
5.41-6.620.0744970.9970.081
6.62-9.370.0483880.9980.0521
9.37-38.710.0372250.9990.0411

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→38.71 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2647 1811 9.99 %
Rwork0.2164 --
obs0.2212 18131 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→38.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 125 114 2697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092630
X-RAY DIFFRACTIONf_angle_d1.1083519
X-RAY DIFFRACTIONf_dihedral_angle_d17.7711016
X-RAY DIFFRACTIONf_chiral_restr0.048367
X-RAY DIFFRACTIONf_plane_restr0.007441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.40371460.33771187X-RAY DIFFRACTION98
2.15-2.210.37631350.27981248X-RAY DIFFRACTION100
2.21-2.290.31551380.25481278X-RAY DIFFRACTION100
2.29-2.370.25081380.24831221X-RAY DIFFRACTION100
2.37-2.460.31481370.23881256X-RAY DIFFRACTION100
2.46-2.570.28571470.25291260X-RAY DIFFRACTION100
2.57-2.710.3081340.23511234X-RAY DIFFRACTION100
2.71-2.880.2791310.22461269X-RAY DIFFRACTION100
2.88-3.10.23971480.21671241X-RAY DIFFRACTION100
3.1-3.410.24611350.20331269X-RAY DIFFRACTION100
3.41-3.910.23521380.19061268X-RAY DIFFRACTION100
3.91-4.920.22481370.1761278X-RAY DIFFRACTION100
4.92-38.710.25721470.21021311X-RAY DIFFRACTION100

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